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The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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--no_stats causing different results in some cases in new VEP #1034

Open Stikus opened 3 years ago

Stikus commented 3 years ago

Describe the issue

We continue digging into differences (https://github.com/Ensembl/ensembl-vep/issues/1031) caused by --no_stats workaround from https://github.com/Ensembl/ensembl-vep/issues/818 and found something more interesting. Two files with --no_stats and without it differs not only with MAX_AF_POPS filed (this happening independently of this flag) but in several other lines.

Moreover - when we use our old VEP (99) - we don't have this problem (here is working version):

Versions:
  ensembl              : 99.d3e7d31
  ensembl-funcgen      : 99.0832337
  ensembl-io           : 99.441b05b
  ensembl-variation    : 99.a7f8736
  ensembl-vep          : 99.2

Additional information

When we compared files from 99 version of VEP with 104 version, we found that old files are nearly equal with run result without --no_stats - that was another evidence that this flag causing problems in new version.

System

Full VEP command line

/soft/ensembl-vep-104.3/vep --fork 192 --input_file /outputs/10_1_strelka.PASSonly.mod.vcf --format vcf --cache --dir_cache /ref/.vep --dir_plugins /soft/ensembl-vep-104.3/Plugins --assembly GRCh38 --offline --output_file /outputs/test1/10_1_strelka-PASSonly-mod.annot-vep.vcf --vcf --no_stats --force_ove
rwrite --symbol --check_existing --terms SO --tsl --hgvs --hgvsg --transcript_version --failed 1 --af --max_af --af_1kg --af_esp --af_gnomad --pubmed --sift b --polyphen b --variant_class --gene_phenotype --regulatory --numbers --domains --protein --canonical --ccds --uniprot --biotype --shift_hgvs 1 --xref_refseq -
-flag_pick_allele --no_escape --minimal --allele_number --total_length

Data files (if applicable)

Our input file (with little truncated header):

##fileformat=VCFv4.1
##fileDate=20200815
##source=strelka
##source_version=2.9.10
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr14,length=107043718>
##content=strelka germline small-variant calls
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant multi-site block. Non-variant blocks are defined independently for each sample. All sites in such a block are constrained to be non-variant, have the same filter value, and have sample values {GQX,DP,DPF} in range [x,y], y <= max(x+3,(x*1.3)).">
##INFO=<ID=SNVHPOL,Number=1,Type=Integer,Description="SNV contextual homopolymer length">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=RU,Number=A,Type=String,Description="Smallest repeating sequence unit extended or contracted in the indel allele relative to the reference. RUs are not reported if longer than 20 bases">
##INFO=<ID=REFREP,Number=A,Type=Integer,Description="Number of times RU is repeated in reference">
##INFO=<ID=IDREP,Number=A,Type=Integer,Description="Number of times RU is repeated in indel allele">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS of mapping quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Empirically calibrated genotype quality score for variant sites, otherwise minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping. In a non-variant multi-site block this value represents the average of all sites in the block.">
##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping. In a non-variant multi-site block this value represents the average of all sites in the block.">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum filtered basecall depth used for site genotyping within a non-variant multi-site block">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.51 or higher that read contains indicated allele vs all other intersecting indel alleles)">
##FORMAT=<ID=ADF,Number=.,Type=Integer,Description="Allelic depths on the forward strand">
##FORMAT=<ID=ADR,Number=.,Type=Integer,Description="Allelic depths on the reverse strand">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
##FORMAT=<ID=DPI,Number=1,Type=Integer,Description="Read depth associated with indel, taken from the site preceding the indel">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase set identifier">
##FORMAT=<ID=SB,Number=1,Type=Float,Description="Sample site strand bias">
##FILTER=<ID=IndelConflict,Description="Indel genotypes from two or more loci conflict in at least one sample">
##FILTER=<ID=SiteConflict,Description="Site is filtered due to an overlapping indel call filter">
##FILTER=<ID=LowGQX,Description="Locus GQX is below threshold or not present">
##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.4">
##FILTER=<ID=HighSNVSB,Description="Sample SNV strand bias value (SB) exceeds 10">
##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth">
##Depth_chr14=36.00
##Depth_chr3=36.00
##FILTER=<ID=LowDepth,Description="Locus depth is below 3">
##FILTER=<ID=NotGenotyped,Description="Locus contains forcedGT input alleles which could not be genotyped">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
##FILTER=<ID=NoPassedVariantGTs,Description="No samples at this locus pass all sample filters and have a variant genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  10_1_S19
chr3    42210085        .       C       CGGAGGA,CGGA    359     PASS    CIGAR=1M6I,1M3I;RU=GGA,GGA;REFREP=10,10;IDREP=12,11;MQ=60       GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:23:7:30:0,16,5:0,10,3:0,6,2:PASS:380,82,31,267,0,235
chr14   24300643        .       A       AGAGGAG,AGAG    694     PASS    CIGAR=1M6I,1M3I;RU=GAG,GAG;REFREP=8,8;IDREP=10,9;MQ=60  GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:224:17:51:0,20,19:0,11,8:0,9,11:PASS:727,318,237,336,0,256

Results: VEP 99 (with our without --no_stats - they are equal):

##VEP="v99" time="2021-08-05 14:38:16" cache="/ref/.vep/homo_sapiens/99_GRCh38" ensembl-funcgen=99.0832337 ensembl-io=99.441b05b ensembl=99.d3e7d31 ensembl-variation=99.a7f8736 1000genomes="phase3" COSMIC="90" ClinVar="201909" ESP="V2-SSA137" HGMD-PUBLIC="20184" assembly="GRCh38.p13" dbSNP="153" gencode="GENCODE 33"
 genebuild="2014-07" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT
_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|HGVSg|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF
|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  10_1_S19
chr3    42210085        .       C       CGGAGGA,CGGA    359     PASS    CIGAR=1M6I,1M3I;RU=GGA,GGA;REFREP=10,10;IDREP=12,11;MQ=60;CSQ=GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000327628.10|protein_coding||14/15|ENST00000327628.10:c.1963+127_1963+132dup|||||||rs10634555|1||1||1|insertion||
HGNC|HGNC:29947|YES|1|CCDS43072.1|ENSP00000328998|Q9UPV9|A0A024R2M0|UPI0000139F52|NM_001349247.2&NM_001042646.3&NM_001349246.2&NM_001265608.2|1||||32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565||||,GGA|intron_variant|MODIFIER|TRAK1|EN
SG00000182606|Transcript|ENST00000327628.10|protein_coding||14/15|ENST00000327628.10:c.1963+130_1963+132dup|||||||rs10634555|2||1||1|insertion||HGNC|HGNC:29947|YES|1|CCDS43072.1|ENSP00000328998|Q9UPV9|A0A024R2M0|UPI0000139F52|NM_001349247.2&NM_001042646.3&NM_001349246.2&NM_001265608.2|1||||32|chr3:g.42210115_4221011
7dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||,GGAGGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1916_1921dup|ENSP00000340702.3:p.Glu639_Glu640dup|2082-2083/4620|1889-1890/2061|63
0/686|T/TEE|acg/acGGAGGAg|rs10634555|1||1|||insertion||HGNC|HGNC:29947||1|CCDS2695.1|ENSP00000340702|Q9UPV9||UPI000034ECE0|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.387
1|gnomAD_AMR||||19837565||||,GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1919_1921dup|ENSP00000340702.3:p.Glu640dup|2082-2083/4620|1889-1890/2061|630/686|T/TE|acg/acGGAg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||1|CCDS2695.1|ENSP0000
0340702|Q9UPV9||UPI000034ECE0|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|
ENST00000396175.5|protein_coding||13/14|ENST00000396175.5:c.1789+127_1789+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||5||ENSP00000379478||C9JC32|UPI000022BFEF||1||||32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565||||,GGA
|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000396175.5|protein_coding||13/14|ENST00000396175.5:c.1789+130_1789+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||5||ENSP00000379478||C9JC32|UPI000022BFEF||1||||32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.319
4|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000487159.5|protein_coding||15/16|ENST00000487159.5:c.1651+127_1651+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||5||ENSP00000486713||A0A0D9SFL5|UPI000387C561|NM_001349245.1&NM_00
1349249.1&NM_001349248.1|1||||32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000487159.5|protein_coding||15/16|ENST00000487159.5:c.1651+130_1651+132dup|||||||rs106
34555|2||1|||insertion||HGNC|HGNC:29947||5||ENSP00000486713||A0A0D9SFL5|UPI000387C561|NM_001349245.1&NM_001349249.1&NM_001349248.1|1||||32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||,GGAGGA|inframe_insertion|MODERATE|TRAK1|ENSG000
00182606|Transcript|ENST00000613405.4|protein_coding|13/13||ENST00000613405.4:c.1868_1873dup|ENSP00000483516.1:p.Glu623_Glu624dup|2142-2143/4672|1841-1842/2013|614/670|T/TEE|acg/acGGAGGAg|rs10634555|1||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0N0|UPI000264F475|NM_001265609.1|1|||MobiDB_l
ite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565||||,GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000613405.4|protein_coding|13/13||ENST0000061340
5.4:c.1871_1873dup|ENSP00000483516.1:p.Glu624dup|2142-2143/4672|1841-1842/2013|614/670|T/TE|acg/acGGAg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0N0|UPI000264F475|NM_001265609.1|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_4
2210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000672026.1|protein_coding||15/17|ENST00000672026.1:c.1651+127_1651+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||||ENSP
00000500099|||||1||||32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000672026.1|protein_coding||15/17|ENST00000672026.1:c.1651+130_1651+132dup|||||||rs10634555|2||
1|||insertion||HGNC|HGNC:29947||||ENSP00000500099|||||1||||32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000673621.1|protein_coding||15/16|ENST00000673621.1:c.
2047+127_2047+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||||ENSP00000500819|||||1||||32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000673621.1|prot
ein_coding||15/16|ENST00000673621.1:c.2047+130_2047+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||||ENSP00000500819|||||1||||32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565||||  GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:23:7:30:
0,16,5:0,10,3:0,6,2:PASS:380,82,31,267,0,235
chr14   24300643        .       A       AGAGGAG,AGAG    694     PASS    CIGAR=1M6I,1M3I;RU=GAG,GAG;REFREP=8,8;IDREP=10,9;MQ=60;CSQ=GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000258807.5|protein_coding||||||||||rs71119069|1|4543|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP000
00258807|Q9UHD4||UPI0000001BDD|NM_014430.3||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000258807.5|protein_coding||||||||||rs71119069|2|4543|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP00000258807|Q9UHD4||UPI0000001BDD
|NM_014430.3||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000267425.8|protein_coding|2/10||ENST00000267425.8:c.504_509dup|ENSP00000267425.3:p.Glu168_Glu169dup|588-589/6045|483-484/1911|161-162/636|-/EE|-/GAGGAG|rs71119069|1||1||1
|insertion||HGNC|HGNC:19826|YES|1|CCDS9624.1|ENSP00000267425|Q86U38||UPI000000CBCF|NM_174913.3||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000267425.8|protein_coding|2/10||E
NST00000267425.8:c.507_509dup|ENSP00000267425.3:p.Glu169dup|588-589/6045|483-484/1911|161-162/636|-/E|-/GAG|rs71119069|2||1||1|insertion||HGNC|HGNC:19826|YES|1|CCDS9624.1|ENSP00000267425|Q86U38||UPI000000CBCF|NM_174913.3||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup|||||
||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000288111.12|protein_coding||||||||||rs71119069|1|863|-1|||insertion||HGNC|HGNC:16445||1|CCDS9623.1|ENSP00000288111|Q96LJ7||UPI000000CBD1|NM_001136050.3||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG
|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000288111.12|protein_coding||||||||||rs71119069|2|863|-1|||insertion||HGNC|HGNC:16445||1|CCDS9623.1|ENSP00000288111|Q96LJ7||UPI000000CBD1|NM_001136050.3||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|M
ODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000336557.9|protein_coding||||||||||rs71119069|1|4543|-1|||insertion||HGNC|HGNC:1977|YES|2|CCDS32056.1|ENSP00000337731|Q9UHD4||UPI0000001BDD|NM_001318807.2||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG000001
36305|Transcript|ENST00000336557.9|protein_coding||||||||||rs71119069|2|4543|-1|||insertion||HGNC|HGNC:1977|YES|2|CCDS32056.1|ENSP00000337731|Q9UHD4||UPI0000001BDD|NM_001318807.2||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST0000039
6802.7|protein_coding|2/10||ENST00000396802.7:c.504_509dup|ENSP00000380020.3:p.Glu168_Glu169dup|559-560/1942|483-484/1608|161-162/535|-/EE|-/GAGGAG|rs71119069|1||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U38||UPI0000E59B3C|NM_001286367.2||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48
371|26|chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.507_509dup|ENSP00000380020.3:p.Glu169dup|559-560/1942|483-484/1608|161-162/535|-/E|-/GAG|rs71119069|2||1|||insertion||HGNC|HGNC:1982
6||5|CCDS66616.1|ENSP00000380020|Q86U38||UPI0000E59B3C|NM_001286367.2||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000396813.5|protein_coding||||||||||rs71119069|1|11
83|-1|||insertion||HGNC|HGNC:16445|YES|2|CCDS9623.1|ENSP00000380027|Q96LJ7||UPI000000CBD1|NM_138452.2||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000396813.5|protein_coding||||||||||rs71119069|2|1183|-1|||insertion||HGNC|HGNC:
16445|YES|2|CCDS9623.1|ENSP00000380027|Q96LJ7||UPI000000CBD1|NM_138452.2||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000554411.5|protein_coding||||||||||rs71119069|1|4452|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP
00000451089|Q9UHD4||UPI0000001BDD|||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000554411.5|protein_coding||||||||||rs71119069|2|4452|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP00000451089|Q9UHD4||UPI0000001BDD|||||||c
hr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000556756.1|protein_coding||||||||||rs71119069|1|4962|-1|cds_start_NF||insertion||HGNC|HGNC:1977||5||ENSP00000451744||G3V4E2|UPI0003B927F0|||||||chr14:g.24300664_24300669dup||||||||||
|||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000556756.1|protein_coding||||||||||rs71119069|2|4962|-1|cds_start_NF||insertion||HGNC|HGNC:1977||5||ENSP00000451744||G3V4E2|UPI0003B927F0|||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_v
ariant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000557362.1|protein_coding||||||||||rs71119069|1|1761|1|cds_start_NF||insertion||HGNC|HGNC:19826||5||ENSP00000451905||H0YJP7|UPI00021CF2EC|||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transc
ript|ENST00000557362.1|protein_coding||||||||||rs71119069|2|1761|1|cds_start_NF||insertion||HGNC|HGNC:19826||5||ENSP00000451905||H0YJP7|UPI00021CF2EC|||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558114.1|retained_intron|
|||||||||rs71119069|1|874|-1|||insertion||HGNC|HGNC:16445||2||||||||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558114.1|retained_intron||||||||||rs71119069|2|874|-1|||insertion||HGNC|HGNC:16445||2||||||||||||chr14:g.2430066
7_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558340.1|nonsense_mediated_decay||||||||||rs71119069|1|900|-1|||insertion||HGNC|HGNC:16445||5||ENSP00000453949||H0YNC2|UPI0000EE4B0F|||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,G
AG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558340.1|nonsense_mediated_decay||||||||||rs71119069|2|900|-1|||insertion||HGNC|HGNC:16445||5||ENSP00000453949||H0YNC2|UPI0000EE4B0F|||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|EN
SG00000157379|Transcript|ENST00000559483.5|processed_transcript||||||||||rs71119069|1|951|-1|||insertion||HGNC|HGNC:16445||3||||||||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000559483.5|processed_transcript||||||||||rs7111906
9|2|951|-1|||insertion||HGNC|HGNC:16445||3||||||||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000560991.1|retained_intron||||||||||rs71119069|1|892|-1|||insertion||HGNC|HGNC:16445||2||||||||||||chr14:g.24300664_24300669dup||
|||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000560991.1|retained_intron||||||||||rs71119069|2|892|-1|||insertion||HGNC|HGNC:16445||2||||||||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|T
ranscript|ENST00000561273.5|retained_intron||||||||||rs71119069|1|882|-1|||insertion||HGNC|HGNC:16445||5||||||||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000561273.5|retained_intron||||||||||rs71119069|2|882|-1|||insertion||H
GNC|HGNC:16445||5||||||||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000650565.1|nonsense_mediated_decay||||||||||rs71119069|1|33|1|cds_start_NF||insertion||HGNC|HGNC:19826||||ENSP00000497287||A0A3B3ISH6|UPI000E6EB091|||||||c
hr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000650565.1|nonsense_mediated_decay||||||||||rs71119069|2|33|1|cds_start_NF||insertion||HGNC|HGNC:19826||||ENSP00000497287||A0A3B3ISH6|UPI000E6EB091|||||||chr14:g.24300667_24300669dup||||||
|||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|AL096870.10|ENSG00000288044|Transcript|ENST00000669726.1|lncRNA||||||||||rs71119069|1|1797|1|||insertion||Clone_based_ensembl_gene||YES|||||||||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|AL096870.10|EN
SG00000288044|Transcript|ENST00000669726.1|lncRNA||||||||||rs71119069|2|1797|1|||insertion||Clone_based_ensembl_gene||YES|||||||||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||,GAGGAG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066854|promoter||||||||||rs71119069|1|||||insertion|||||
||||||||||||chr14:g.24300664_24300669dup|||||||||||||||||||||||||||,GAG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066854|promoter||||||||||rs71119069|2|||||insertion|||||||||||||||||chr14:g.24300667_24300669dup|||||||||||||||||||||||||||       GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:224:17:51:0,20,
19:0,11,8:0,9,11:PASS:727,318,237,336,0,256

VEP 104 (with --no_stats):

##VEP="v104" time="2021-08-05 14:21:46" cache="/ref/.vep/homo_sapiens/104_GRCh38" ensembl-io=104.1d3bb6e ensembl-funcgen=104.59ae779 ensembl-variation=104.6154f8b ensembl=104.1af1dce 1000genomes="phase3" COSMIC="92" ClinVar="20210102" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GEN
CODE 38" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT
_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|HGVSg|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_
AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  10_1_S19
chr3    42210085        .       C       CGGAGGA,CGGA    359     PASS    CIGAR=1M6I,1M3I;RU=GGA,GGA;REFREP=10,10;IDREP=12,11;MQ=60;CSQ=GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000327628.10|protein_coding||14/15|ENST00000327628.10:c.1963+127_1963+132dup|||||||rs10634555|1||1||1|insertion||
HGNC|HGNC:29947|YES|1|CCDS43072.1|ENSP00000328998|Q9UPV9.163||UPI0000139F52|Q9UPV9-1|NM_001349247.2&NM_001042646.3&NM_001349246.2&NM_001265608.2|1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|
ENSG00000182606|Transcript|ENST00000327628.10|protein_coding||14/15|ENST00000327628.10:c.1963+130_1963+132dup|||||||rs10634555|2||1||1|insertion||HGNC|HGNC:29947|YES|1|CCDS43072.1|ENSP00000328998|Q9UPV9.163||UPI0000139F52|Q9UPV9-1|NM_001349247.2&NM_001042646.3&NM_001349246.2&NM_001265608.2|1|||||chr3:g.42210115_4221
0117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1916_1921dup|ENSP00000340702.3:p.Glu639_Glu640dup|2082-2083/4620|1889-1890/206
1|630/686|T/TEE|acg/acGGAGGAg|rs10634555|1||1|||insertion||HGNC|HGNC:29947||1|CCDS2695.1|ENSP00000340702|Q9UPV9.163||UPI000034ECE0|Q9UPV9-2|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.
2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1919_1921dup|ENSP00000340702.3:p.Glu640dup|2082-2083/4620|1921-1922/2061|641/686|G/GR|acg/ggGAGg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||1|C
CDS2695.1|ENSP00000340702|Q9UPV9.163||UPI000034ECE0|Q9UPV9-2|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_variant|MODIFIER|T
RAK1|ENSG00000182606|Transcript|ENST00000396175.5|protein_coding||13/14|ENST00000396175.5:c.1789+127_1789+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||5||ENSP00000379478||C9JC32.90|UPI000022BFEF|||1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3
871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000396175.5|protein_coding||13/14|ENST00000396175.5:c.1789+130_1789+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||5||ENSP00000379478||C9JC32.90|UPI000022BFEF|||1|||||chr3:g.42210115_42210117dup|||||||||0.2
744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000487159.5|protein_coding||15/16|ENST00000487159.5:c.1651+127_1651+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||5||ENSP00000486713||A0A0D9S
FL5.36|UPI000387C561||NM_001349245.1&NM_001349249.1&NM_001349248.1|1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000487159.5|protein_coding||15/16|ENST0000048
7159.5:c.1651+130_1651+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||5||ENSP00000486713||A0A0D9SFL5.36|UPI000387C561||NM_001349245.1&NM_001349249.1&NM_001349248.1|1|||||chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGA
GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000613405.4|protein_coding|13/13||ENST00000613405.4:c.1868_1873dup|ENSP00000483516.1:p.Glu623_Glu624dup|2142-2143/4672|1841-1842/2013|614/670|T/TEE|acg/acGGAGGAg|rs10634555|1||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0
N0.42|UPI000264F475||NM_001265609.2|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST0
0000613405.4|protein_coding|13/13||ENST00000613405.4:c.1871_1873dup|ENSP00000483516.1:p.Glu624dup|2142-2143/4672|1873-1874/2013|625/670|G/GR|acg/ggGAGg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0N0.42|UPI000264F475||NM_001265609.2|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobi
db-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000672026.1|protein_coding||15/17|ENST00000672026.1:c.1651+127_1651+132dup|||||
||rs10634555|1||1|||insertion||HGNC|HGNC:29947||||ENSP00000500099||A0A5F9ZH95.5|UPI00123701F0|||1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000672026.1|prot
ein_coding||15/17|ENST00000672026.1:c.1651+130_1651+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||||ENSP00000500099||A0A5F9ZH95.5|UPI00123701F0|||1|||||chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_varian
t|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000673621.2|protein_coding||15/16|ENST00000673621.2:c.2047+127_2047+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||||ENSP00000500819||A0A5F9ZI06.5||||1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.
3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000673621.2|protein_coding||15/16|ENST00000673621.2:c.2047+130_2047+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||||ENSP00000500819||A0A5F9ZI06.5||||1|||||chr3:g.42210115_42210117dup|||||||||0.2744|0.3133
|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||  GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:23:7:30:0,16,5:0,10,3:0,6,2:PASS:380,82,31,267,0,235
chr14   24300643        .       A       AGAGGAG,AGAG    694     PASS    CIGAR=1M6I,1M3I;RU=GAG,GAG;REFREP=8,8;IDREP=10,9;MQ=60;CSQ=GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000258807.5|protein_coding||||||||||rs71119069|1|4543|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP000
00258807|Q9UHD4.165||UPI0000001BDD||NM_014430.3||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000258807.5|protein_coding||||||||||rs71119069|2|4543|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP00000258807|Q9UHD4.165||UPI
0000001BDD||NM_014430.3||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000267425.8|protein_coding|2/10||ENST00000267425.8:c.504_509dup|ENSP00000267425.3:p.Glu168_Glu169dup|588-589/6045|483-484/1911|161-162/636|-/EE|-/GAGGAG|rs7111
9069|1||1||1|insertion||HGNC|HGNC:19826|YES|1|CCDS9624.1|ENSP00000267425|Q86U38.144||UPI000000CBCF|Q86U38-1|NM_174913.3||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST0000026742
5.8|protein_coding|2/10||ENST00000267425.8:c.507_509dup|ENSP00000267425.3:p.Glu169dup|588-589/6045|509-510/1911|170/636|D/E|-/GAG|rs71119069|2||1||1|insertion||HGNC|HGNC:19826|YES|1|CCDS9624.1|ENSP00000267425|Q86U38.144||UPI000000CBCF|Q86U38-1|NM_174913.3||tolerated(0.84)|benign(0.001)|Gene3D:1.25.10.10&PANTHER:PTHR
13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000288111.12|protein_coding||||||||||rs71119069|1|863|-1|||insertion||HGNC|HGNC:16445|YES|1|CCDS9623.1|ENSP00000288111|Q96LJ7.153||UPI000000CBD1||NM_0011
36050.3||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000288111.12|protein_coding||||||||||rs71119069|2|863|-1|||insertion||HGNC|HGNC:16445|YES|1|CCDS9623.1|ENSP00000288111|Q96LJ7.153||UPI000000CBD1||NM_001136050.3||||||chr14:g
.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000336557.9|protein_coding||||||||||rs71119069|1|4543|-1|||insertion||HGNC|HGNC:1977||2|CCDS32056.1|ENSP00000337731|Q9UHD4.165||UPI0000001BDD||NM_001318807.2||||||chr14:g.24300664_24300669
dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000336557.9|protein_coding||||||||||rs71119069|2|4543|-1|||insertion||HGNC|HGNC:1977||2|CCDS32056.1|ENSP00000337731|Q9UHD4.165||UPI0000001BDD||NM_001318807.2||||||chr14:g.24300667_24300669dup||||||||||||||||||
||||||||||,GAGGAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.504_509dup|ENSP00000380020.3:p.Glu168_Glu169dup|559-560/1942|483-484/1608|161-162/535|-/EE|-/GAGGAG|rs71119069|1||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U3
8.144||UPI0000E59B3C|Q86U38-2|NM_001286367.2||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|protein_altering_variant|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.507_509dup|ENSP00000380
020.3:p.Glu169dup|559-560/1942|509-510/1608|170/535|D/ES|-/GAGagt|rs71119069|2||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U38.144||UPI0000E59B3C|Q86U38-2|NM_001286367.2||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGA
G|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000396813.5|protein_coding||||||||||rs71119069|1|1183|-1|||insertion||HGNC|HGNC:16445||2|CCDS9623.1|ENSP00000380027|Q96LJ7.153||UPI000000CBD1||NM_138452.3||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MO
DIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000396813.5|protein_coding||||||||||rs71119069|2|1183|-1|||insertion||HGNC|HGNC:16445||2|CCDS9623.1|ENSP00000380027|Q96LJ7.153||UPI000000CBD1||NM_138452.3||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG0000
0136305|Transcript|ENST00000554411.5|protein_coding||||||||||rs71119069|1|4452|-1|||insertion||HGNC|HGNC:1977|YES|1|CCDS32056.1|ENSP00000451089|Q9UHD4.165||UPI0000001BDD||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST000005544
11.5|protein_coding||||||||||rs71119069|2|4452|-1|||insertion||HGNC|HGNC:1977|YES|1|CCDS32056.1|ENSP00000451089|Q9UHD4.165||UPI0000001BDD||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000556756.1|protein_coding||||||||||
rs71119069|1|4962|-1|cds_start_NF||insertion||HGNC|HGNC:1977||5||ENSP00000451744||G3V4E2.40|UPI0003B927F0||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000556756.1|protein_coding||||||||||rs71119069|2|4962|-1|cds_start_NF||
insertion||HGNC|HGNC:1977||5||ENSP00000451744||G3V4E2.40|UPI0003B927F0||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000557362.1|protein_coding||||||||||rs71119069|1|1761|1|cds_start_NF||insertion||HGNC|HGNC:19826||5||ENSP0
0000451905||H0YJP7.43|UPI00021CF2EC||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000557362.1|protein_coding||||||||||rs71119069|2|1761|1|cds_start_NF||insertion||HGNC|HGNC:19826||5||ENSP00000451905||H0YJP7.43|UPI00021CF2EC|||
|||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558114.1|retained_intron||||||||||rs71119069|1|874|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_va
riant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558114.1|retained_intron||||||||||rs71119069|2|874|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558340.1|nonsense_mediate
d_decay||||||||||rs71119069|1|900|-1|||insertion||HGNC|HGNC:16445||5||ENSP00000453949||H0YNC2.71|UPI0000EE4B0F||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558340.1|nonsense_mediated_decay||||||||||rs71119069|2|900|-1|||i
nsertion||HGNC|HGNC:16445||5||ENSP00000453949||H0YNC2.71|UPI0000EE4B0F||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000559483.5|processed_transcript||||||||||rs71119069|1|951|-1|||insertion||HGNC|HGNC:16445||3||||||||||||
|chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000559483.5|processed_transcript||||||||||rs71119069|2|951|-1|||insertion||HGNC|HGNC:16445||3|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_v
ariant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000560991.1|retained_intron||||||||||rs71119069|1|892|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000560991.1|retained_intron|||
|||||||rs71119069|2|892|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000561273.5|retained_intron||||||||||rs71119069|1|882|-1|||insertion||HGNC|HGNC:16445||5|||||||||||||chr14:g.243
00664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000561273.5|retained_intron||||||||||rs71119069|2|882|-1|||insertion||HGNC|HGNC:16445||5|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|N
OP9|ENSG00000196943|Transcript|ENST00000650565.1|nonsense_mediated_decay||||||||||rs71119069|1|33|1|cds_start_NF||insertion||HGNC|HGNC:19826||||ENSP00000497287||A0A3B3ISH6.9|UPI000E6EB091||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcrip
t|ENST00000650565.1|nonsense_mediated_decay||||||||||rs71119069|2|33|1|cds_start_NF||insertion||HGNC|HGNC:19826||||ENSP00000497287||A0A3B3ISH6.9|UPI000E6EB091||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER||ENSG00000288044|Transcript|ENST00000669726.1|lncRNA||
||||||||rs71119069|1|1797|1|||insertion||||YES||||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER||ENSG00000288044|Transcript|ENST00000669726.1|lncRNA||||||||||rs71119069|2|1797|1|||insertion||||YES||||||||||||||chr14:g.24300667_24300669dup|||||||||||||||||||||
|||||||,GAGGAG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066854|promoter||||||||||rs71119069|1|||||insertion||||||||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066854|promoter||||||||||rs71119069|2|||||in
sertion||||||||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||    GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:224:17:51:0,20,19:0,11,8:0,9,11:PASS:727,318,237,336,0,256

VEP 104 (without --no_stats):

##VEP="v104" time="2021-08-05 14:23:39" cache="/ref/.vep/homo_sapiens/104_GRCh38" ensembl=104.1af1dce ensembl-funcgen=104.59ae779 ensembl-io=104.1d3bb6e ensembl-variation=104.6154f8b 1000genomes="phase3" COSMIC="92" ClinVar="20210102" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GEN
CODE 38" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT
_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|HGVSg|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_
AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  10_1_S19
chr3    42210085        .       C       CGGAGGA,CGGA    359     PASS    CIGAR=1M6I,1M3I;RU=GGA,GGA;REFREP=10,10;IDREP=12,11;MQ=60;CSQ=GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000327628.10|protein_coding||14/15|ENST00000327628.10:c.1963+127_1963+132dup|||||||rs10634555|1||1||1|insertion||
HGNC|HGNC:29947|YES|1|CCDS43072.1|ENSP00000328998|Q9UPV9.163||UPI0000139F52|Q9UPV9-1|NM_001349247.2&NM_001042646.3&NM_001349246.2&NM_001265608.2|1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|
ENSG00000182606|Transcript|ENST00000327628.10|protein_coding||14/15|ENST00000327628.10:c.1963+130_1963+132dup|||||||rs10634555|2||1||1|insertion||HGNC|HGNC:29947|YES|1|CCDS43072.1|ENSP00000328998|Q9UPV9.163||UPI0000139F52|Q9UPV9-1|NM_001349247.2&NM_001042646.3&NM_001349246.2&NM_001265608.2|1|||||chr3:g.42210115_4221
0117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1916_1921dup|ENSP00000340702.3:p.Glu639_Glu640dup|2082-2083/4620|1889-1890/206
1|630/686|T/TEE|acg/acGGAGGAg|rs10634555|1||1|||insertion||HGNC|HGNC:29947||1|CCDS2695.1|ENSP00000340702|Q9UPV9.163||UPI000034ECE0|Q9UPV9-2|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.
2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1919_1921dup|ENSP00000340702.3:p.Glu640dup|2082-2083/4620|1921-1922/2061|641/686|G/TE|acg/acGGAg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||1|C
CDS2695.1|ENSP00000340702|Q9UPV9.163||UPI000034ECE0|Q9UPV9-2|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_variant|MODIFIER|T
RAK1|ENSG00000182606|Transcript|ENST00000396175.5|protein_coding||13/14|ENST00000396175.5:c.1789+127_1789+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||5||ENSP00000379478||C9JC32.90|UPI000022BFEF|||1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3
871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000396175.5|protein_coding||13/14|ENST00000396175.5:c.1789+130_1789+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||5||ENSP00000379478||C9JC32.90|UPI000022BFEF|||1|||||chr3:g.42210115_42210117dup|||||||||0.2
744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000487159.5|protein_coding||15/16|ENST00000487159.5:c.1651+127_1651+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||5||ENSP00000486713||A0A0D9S
FL5.36|UPI000387C561||NM_001349245.1&NM_001349249.1&NM_001349248.1|1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000487159.5|protein_coding||15/16|ENST0000048
7159.5:c.1651+130_1651+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||5||ENSP00000486713||A0A0D9SFL5.36|UPI000387C561||NM_001349245.1&NM_001349249.1&NM_001349248.1|1|||||chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGA
GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000613405.4|protein_coding|13/13||ENST00000613405.4:c.1868_1873dup|ENSP00000483516.1:p.Glu623_Glu624dup|2142-2143/4672|1841-1842/2013|614/670|T/TEE|acg/acGGAGGAg|rs10634555|1||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0
N0.42|UPI000264F475||NM_001265609.2|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST0
0000613405.4|protein_coding|13/13||ENST00000613405.4:c.1871_1873dup|ENSP00000483516.1:p.Glu624dup|2142-2143/4672|1873-1874/2013|625/670|G/TE|acg/acGGAg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0N0.42|UPI000264F475||NM_001265609.2|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobi
db-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000672026.1|protein_coding||15/17|ENST00000672026.1:c.1651+127_1651+132dup|||||
||rs10634555|1||1|||insertion||HGNC|HGNC:29947||||ENSP00000500099||A0A5F9ZH95.5|UPI00123701F0|||1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000672026.1|prot
ein_coding||15/17|ENST00000672026.1:c.1651+130_1651+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||||ENSP00000500099||A0A5F9ZH95.5|UPI00123701F0|||1|||||chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||,GGAGGA|intron_varian
t|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000673621.2|protein_coding||15/16|ENST00000673621.2:c.2047+127_2047+132dup|||||||rs10634555|1||1|||insertion||HGNC|HGNC:29947||||ENSP00000500819||A0A5F9ZI06.5||||1|||||chr3:g.42210112_42210117dup|||||||||0.2527|0.217|0.3871|0.2029|0.351|0.1962|0.2198|0.2555|0.2385|0.
3871|gnomAD_AMR||||19837565|||||,GGA|intron_variant|MODIFIER|TRAK1|ENSG00000182606|Transcript|ENST00000673621.2|protein_coding||15/16|ENST00000673621.2:c.2047+130_2047+132dup|||||||rs10634555|2||1|||insertion||HGNC|HGNC:29947||||ENSP00000500819||A0A5F9ZI06.5||||1|||||chr3:g.42210115_42210117dup|||||||||0.2744|0.3133
|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492|gnomAD_EAS||||19837565|||||  GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:23:7:30:0,16,5:0,10,3:0,6,2:PASS:380,82,31,267,0,235
chr14   24300643        .       A       AGAGGAG,AGAG    694     PASS    CIGAR=1M6I,1M3I;RU=GAG,GAG;REFREP=8,8;IDREP=10,9;MQ=60;CSQ=GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000258807.5|protein_coding||||||||||rs71119069|1|4543|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP000
00258807|Q9UHD4.165||UPI0000001BDD||NM_014430.3||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000258807.5|protein_coding||||||||||rs71119069|2|4543|-1|||insertion||HGNC|HGNC:1977||1|CCDS32056.1|ENSP00000258807|Q9UHD4.165||UPI
0000001BDD||NM_014430.3||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000267425.8|protein_coding|2/10||ENST00000267425.8:c.504_509dup|ENSP00000267425.3:p.Glu168_Glu169dup|588-589/6045|483-484/1911|161-162/636|-/EE|-/GAGGAG|rs7111
9069|1||1||1|insertion||HGNC|HGNC:19826|YES|1|CCDS9624.1|ENSP00000267425|Q86U38.144||UPI000000CBCF|Q86U38-1|NM_174913.3||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST0000026742
5.8|protein_coding|2/10||ENST00000267425.8:c.507_509dup|ENSP00000267425.3:p.Glu169dup|588-589/6045|509-510/1911|170/636|D/E|-/GAG|rs71119069|2||1||1|insertion||HGNC|HGNC:19826|YES|1|CCDS9624.1|ENSP00000267425|Q86U38.144||UPI000000CBCF|Q86U38-1|NM_174913.3||tolerated(0.84)|benign(0.001)|Gene3D:1.25.10.10&PANTHER:PTHR
13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000288111.12|protein_coding||||||||||rs71119069|1|863|-1|||insertion||HGNC|HGNC:16445|YES|1|CCDS9623.1|ENSP00000288111|Q96LJ7.153||UPI000000CBD1||NM_0011
36050.3||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000288111.12|protein_coding||||||||||rs71119069|2|863|-1|||insertion||HGNC|HGNC:16445|YES|1|CCDS9623.1|ENSP00000288111|Q96LJ7.153||UPI000000CBD1||NM_001136050.3||||||chr14:g
.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000336557.9|protein_coding||||||||||rs71119069|1|4543|-1|||insertion||HGNC|HGNC:1977||2|CCDS32056.1|ENSP00000337731|Q9UHD4.165||UPI0000001BDD||NM_001318807.2||||||chr14:g.24300664_24300669
dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000336557.9|protein_coding||||||||||rs71119069|2|4543|-1|||insertion||HGNC|HGNC:1977||2|CCDS32056.1|ENSP00000337731|Q9UHD4.165||UPI0000001BDD||NM_001318807.2||||||chr14:g.24300667_24300669dup||||||||||||||||||
||||||||||,GAGGAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.504_509dup|ENSP00000380020.3:p.Glu168_Glu169dup|559-560/1942|483-484/1608|161-162/535|-/EE|-/GAGGAG|rs71119069|1||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U3
8.144||UPI0000E59B3C|Q86U38-2|NM_001286367.2||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.507_509dup|ENSP00000380020.3:p
.Glu169dup|559-560/1942|509-510/1608|170/535|D/E|-/GAG|rs71119069|2||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U38.144||UPI0000E59B3C|Q86U38-2|NM_001286367.2||tolerated(0.9)|benign(0.001)|Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup||||||||||||||||||
||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000396813.5|protein_coding||||||||||rs71119069|1|1183|-1|||insertion||HGNC|HGNC:16445||2|CCDS9623.1|ENSP00000380027|Q96LJ7.153||UPI000000CBD1||NM_138452.3||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream
_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000396813.5|protein_coding||||||||||rs71119069|2|1183|-1|||insertion||HGNC|HGNC:16445||2|CCDS9623.1|ENSP00000380027|Q96LJ7.153||UPI000000CBD1||NM_138452.3||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIE
R|CIDEB|ENSG00000136305|Transcript|ENST00000554411.5|protein_coding||||||||||rs71119069|1|4452|-1|||insertion||HGNC|HGNC:1977|YES|1|CCDS32056.1|ENSP00000451089|Q9UHD4.165||UPI0000001BDD||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcri
pt|ENST00000554411.5|protein_coding||||||||||rs71119069|2|4452|-1|||insertion||HGNC|HGNC:1977|YES|1|CCDS32056.1|ENSP00000451089|Q9UHD4.165||UPI0000001BDD||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000556756.1|protein_
coding||||||||||rs71119069|1|4962|-1|cds_start_NF||insertion||HGNC|HGNC:1977||5||ENSP00000451744||G3V4E2.40|UPI0003B927F0||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER|CIDEB|ENSG00000136305|Transcript|ENST00000556756.1|protein_coding||||||||||rs71119069|2|4962|-
1|cds_start_NF||insertion||HGNC|HGNC:1977||5||ENSP00000451744||G3V4E2.40|UPI0003B927F0||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000557362.1|protein_coding||||||||||rs71119069|1|1761|1|cds_start_NF||insertion||HGNC|HGNC
:19826||5||ENSP00000451905||H0YJP7.43|UPI00021CF2EC||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000557362.1|protein_coding||||||||||rs71119069|2|1761|1|cds_start_NF||insertion||HGNC|HGNC:19826||5||ENSP00000451905||H0YJP7.43|
UPI00021CF2EC||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558114.1|retained_intron||||||||||rs71119069|1|874|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|
upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558114.1|retained_intron||||||||||rs71119069|2|874|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558340.1|
nonsense_mediated_decay||||||||||rs71119069|1|900|-1|||insertion||HGNC|HGNC:16445||5||ENSP00000453949||H0YNC2.71|UPI0000EE4B0F||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000558340.1|nonsense_mediated_decay||||||||||rs71119
069|2|900|-1|||insertion||HGNC|HGNC:16445||5||ENSP00000453949||H0YNC2.71|UPI0000EE4B0F||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000559483.5|processed_transcript||||||||||rs71119069|1|951|-1|||insertion||HGNC|HGNC:1644
5||3|||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000559483.5|processed_transcript||||||||||rs71119069|2|951|-1|||insertion||HGNC|HGNC:16445||3|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG
|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000560991.1|retained_intron||||||||||rs71119069|1|892|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000560991.1|re
tained_intron||||||||||rs71119069|2|892|-1|||insertion||HGNC|HGNC:16445||2|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000561273.5|retained_intron||||||||||rs71119069|1|882|-1|||insertion||HGNC|HGNC:16445||5||||||||
|||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|DHRS1|ENSG00000157379|Transcript|ENST00000561273.5|retained_intron||||||||||rs71119069|2|882|-1|||insertion||HGNC|HGNC:16445||5|||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|upstream_gene_va
riant|MODIFIER|NOP9|ENSG00000196943|Transcript|ENST00000650565.1|nonsense_mediated_decay||||||||||rs71119069|1|33|1|cds_start_NF||insertion||HGNC|HGNC:19826||||ENSP00000497287||A0A3B3ISH6.9|UPI000E6EB091||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|upstream_gene_variant|MODIFIER|NOP9|ENSG00000
196943|Transcript|ENST00000650565.1|nonsense_mediated_decay||||||||||rs71119069|2|33|1|cds_start_NF||insertion||HGNC|HGNC:19826||||ENSP00000497287||A0A3B3ISH6.9|UPI000E6EB091||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||,GAGGAG|downstream_gene_variant|MODIFIER||ENSG00000288044|Transcript|ENST000006
69726.1|lncRNA||||||||||rs71119069|1|1797|1|||insertion||||YES||||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|downstream_gene_variant|MODIFIER||ENSG00000288044|Transcript|ENST00000669726.1|lncRNA||||||||||rs71119069|2|1797|1|||insertion||||YES||||||||||||||chr14:g.24300667_24300669dup|||||
|||||||||||||||||||||||,GAGGAG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066854|promoter||||||||||rs71119069|1|||||insertion||||||||||||||||||chr14:g.24300664_24300669dup||||||||||||||||||||||||||||,GAG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000066854|promoter||||||||||rs7
1119069|2|||||insertion||||||||||||||||||chr14:g.24300667_24300669dup||||||||||||||||||||||||||||    GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:224:17:51:0,20,19:0,11,8:0,9,11:PASS:727,318,237,336,0,256

And here are the differences in transcripts:

< GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1919_1921dup|ENSP00000340702.3:p.Glu640dup|2082-2083/4620|1921-1922/2061|641/686|G/TE|acg/acGGAg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||1|CCDS2695.1|ENSP00000340702|Q9UPV9.163||UPI000034ECE0|Q9UPV9-2|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492||||19837565||||
---
> GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000341421.7|protein_coding|13/13||ENST00000341421.7:c.1919_1921dup|ENSP00000340702.3:p.Glu640dup|2082-2083/4620|1921-1922/2061|641/686|G/GR|acg/ggGAGg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||1|CCDS2695.1|ENSP00000340702|Q9UPV9.163||UPI000034ECE0|Q9UPV9-2|NM_014965.5|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492||||19837565||||
2951c2951
< GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000613405.4|protein_coding|13/13||ENST00000613405.4:c.1871_1873dup|ENSP00000483516.1:p.Glu624dup|2142-2143/4672|1873-1874/2013|625/670|G/TE|acg/acGGAg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0N0.42|UPI000264F475||NM_001265609.2|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492||||19837565||||
---
> GGA|inframe_insertion|MODERATE|TRAK1|ENSG00000182606|Transcript|ENST00000613405.4|protein_coding|13/13||ENST00000613405.4:c.1871_1873dup|ENSP00000483516.1:p.Glu624dup|2142-2143/4672|1873-1874/2013|625/670|G/GR|acg/ggGAGg|rs10634555|2||1|||insertion||HGNC|HGNC:29947||2|CCDS74922.1|ENSP00000483516||A0A087X0N0.42|UPI000264F475||NM_001265609.2|1|||MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|32|chr3:g.42210115_42210117dup|||||||||0.2744|0.3133|0.3166|0.2237|0.4492|0.3194|0.247|0.266|0.1756|0.4492||||19837565||||
10658c10658
< GAG|inframe_insertion|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.507_509dup|ENSP00000380020.3:p.Glu169dup|559-560/1942|509-510/1608|170/535|D/E|-/GAG|rs71119069|2||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U38.144||UPI0000E59B3C|Q86U38-2|NM_001286367.2||tolerated(0.9)|benign(0.001)|Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup||||||||||||||||||||||||||
---
> GAG|protein_altering_variant|MODERATE|NOP9|ENSG00000196943|Transcript|ENST00000396802.7|protein_coding|2/10||ENST00000396802.7:c.507_509dup|ENSP00000380020.3:p.Glu169dup|559-560/1942|509-510/1608|170/535|D/ES|-/GAGagt|rs71119069|2||1|||insertion||HGNC|HGNC:19826||5|CCDS66616.1|ENSP00000380020|Q86U38.144||UPI0000E59B3C|Q86U38-2|NM_001286367.2||||Gene3D:1.25.10.10&PANTHER:PTHR13102&Superfamily:SSF48371|26|chr14:g.24300667_24300669dup||||||||||||||||||||||||||

First two pair are from first line from VCF and here is the different parts - G/TE|acg/acGGAg without --no-stats and G/GR|acg/ggGAGg with. But this is GAA insertion, not GAG - its strange at least.

Last pair has differences not only in amino acids and codons, but in Consequence, SIFT, PolyPhen too.

serge2016 commented 3 years ago

Could you fix this, please?

aparton commented 3 years ago

Hi @Stikus,

Thanks for bringing this to our attention. I can reproduce the issue, and I'll let you know when we have a fix in place.

Kind Regards, Andrew

serge2016 commented 3 years ago

Hi! Any news here? How critical is this inconsistency?

Stikus commented 3 years ago

Hello, any progress about this problem?

dglemos commented 3 years ago

Hi @serge2016 and @Stikus, Unfortunately we do not have a fix in place for this issue yet.

serge2016 commented 3 years ago

Very pity( Hope to see it soon!

Stikus commented 2 years ago

Hello, any news?

I've found closed PR related to this issue: https://github.com/Ensembl/ensembl-vep/pull/1044

We cannot use latest VEP releases in our production due to this problem because without --no-stats runtime is twice longer, and we don't have time for such long pipeline.

ntm commented 2 years ago

Until the issue is fixed, as a workaround you could try a solution similar to https://github.com/ntm/grexome-TIMC-Secondary/blob/master/3_runVEP.pl This is designed for the N+1 case, where you regularly run VEP on new VCFs comprised mostly of variants that were seen in your older VCFs. Briefly, this script constructs/updates a private cache of VEP CSQs for each "chr:pos:ref:alt". Then when parsing a new VCF, any line whose "chr:pos:ref:alt" was seen before will not go through VEP, and instead the CSQ is retrieved from the private cache. In our workloads this provides great speedups, and having to disable --no_stats hsan't hurt us much.

jamie-m-a commented 2 years ago

Hi @Stikus,

We are still working on this I'm afraid, the pull request you refer to was closed because I don't believe it resolved the issue. We will update when a fix is in place. In the meantime, perhaps the workaround suggested by @ntm above can be useful for you.

Cheers, Jamie.

serge2016 commented 2 years ago

Dear authors! Could you please add sorting to this place? I hope to see this fix very much!

jamie-m-a commented 2 years ago

Hi @serge2016

Rather than repeating, can I point you to my answer on ticket 1066 (https://github.com/Ensembl/ensembl-vep/issues/1066) as it also applies to this issue.

serge2016 commented 1 year ago

Dear colleagues, @aparton @dglemos @nuno-agostinho @jamie-m-a, a year more is gone. I really think this bug is critical! What can I do to help? I have no idea, how the --no_stats flag influence results in VCF-file...

nuno-agostinho commented 1 year ago

Hey @serge2016,

We have not advanced further on this issue, but I'll prioritise this. I am sorry for the inconvenience.

Kind regards, Nuno

serge2016 commented 1 year ago

Thank you, @nuno-agostinho Hope to see updates soon! It is really critical bug for us...

serge2016 commented 1 year ago

Dear @nuno-agostinho, Can we hope to see the fix in 110?

nuno-agostinho commented 1 year ago

Hey @Stikus and @serge2016!

I was playing with a quick fix to the issue (https://github.com/Ensembl/ensembl-vep/pull/1427), but it makes VEP with --no_stats take as much time as a normal VEP run, so I will have to investigate this further.

From what I can gather, these issues happen only when using --no_stats together with --hgvs (may be a variant 3-prime shifting issue). I think the inconsistencies reported could be avoided by simply not using the --hgvs flag, if that's possible.

I am trying to find a good way to fix this, but the release 110 is imminent (so probably not going in for 110). Sorry for the inconvenience.

Best, Nuno

Stikus commented 1 year ago

Hello @nuno-agostinho, have you found the fix for this issue?

serge2016 commented 1 week ago

Hello, @jamie-m-a !!! Could you help with this, please?

jamie-m-a commented 1 week ago

Hi @serge2016 from what we've been able to discover, the --no_stats option when used with --hgvs doesn't properly calculate the hgvs in all cases. The only workaround we've found is to recalculate hgvs at the end, but this will negate the speed improvement offered by running with --no_stats.

Unfortunately we don't have capacity in the team at present to fix this issue, so I'd suggest running without --no_stats and look at parallelisation options (such as using the Nextflow VEP pipeline) to improve annotation speed.

serge2016 commented 1 week ago

Thank you! I understand, but hope you'll find a possibility to fix this.