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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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Problem of: Use of uninitialized value #1632

Closed celine-weng closed 3 months ago

celine-weng commented 3 months ago

Describe the issue

3 warning that I got:

STATUS: Running VEP and writing to: HI.snv.vep.vcf

WARNING: 96322 : Use of uninitialized value in string eq at /home/anaconda3/envs/idat2maf/share/ensembl-vep-102.0-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2145, <__ANONIO__> line 13000.

Use of uninitialized value $check_alt in numeric ge (>=) at /home/anaconda3/envs/idat2maf/share/ensembl-vep-102.0-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2148, <__ANONIO__> line 13000.

Use of uninitialized value in uc at /home/anaconda3/envs/idat2maf/lib/site_perl/5.26.2/Bio/SeqUtils.pm line 290, <__ANONIO__> line 13000.

WARNING: No genotype column for NORMAL in VCF!

Additional information

Previously, I run the same command with same file, but on different computer and different reference. Previously I used GRCh37 and it work well without any warning. But when I tried to run it with GRCh38, it output those three warnings. I don't know if this is related to the problem or not. I could get the output, but I'm not sure if this warning will affect my output. I used the vcf file generated from SnpEff as input file.

System

Full VEP command line

vep --species homo_sapiens --assembly GRCh38 --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /.vep --fasta /.vep/homo_sapiens/102_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --format vcf --input_file HI.snv.vcf --output_file HI.snv.vep.vcf --offline --pubmed --fork 4 --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory
likhitha-surapaneni commented 3 months ago

Hi @celine-weng , Thank you for reaching out. Can you please provide an input file?

celine-weng commented 3 months ago

Due to privacy reason, I can provide you with some sample, will this be enough?

fileformat=VCFv4.1

source=array-analysis-cli 2.1.0

genomeBuild=38

reference=file://GRCh38_latest_genomic.fa

FORMAT=

FORMAT=

FORMAT=

FORMAT=

contig=

contig=

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contig=

contig=

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contig=

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contig=

contig=

contig=

SnpEffVersion="5.2a (build 2023-10-24 14:24), by Pablo Cingolani"

SnpEffCmd="SnpEff GRCh38.105 /home/idat2maf/idat_sample/vcf/sample.snv.vcf "

INFO=

INFO=

INFO=

SnpSiftVersion="SnpSift 5.2 (build 2023-10-24 14:25), by Pablo Cingolani"

SnpSiftCmd="SnpSift Filter 'ANN[*].IMPACT has 'HIGH'' /home/idat2maf/idat_sample/vcf/snpEff_annotated_vcf/sample.snpEff.ann.snv.vcf"

FILTER=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample

1 980192 1:915572 CTG C . PASS ANN=C|frameshift_variant|HIGH|PERM1|ENSG00000187642|transcript|ENST00000341290.6|protein_coding|3/5|c.494_495delCA|p.Thr165fs|531/3035|494/2031|165/676||,C|frameshift_variant|HIGH|PERM1|ENSG00000187642|transcript|ENST00000433179.3|protein_coding|1/3|c.836_837delCA|p.Thr279fs|837/3340|836/2373|279/790||,C|upstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|transcript|ENST00000479361.1|retainedintron||n.-3553-3552delCA|||||3552|,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000379410.8|proteincoding||c.*56185619delTG|||||4328|,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|transcript|ENST00000491024.1|protein_coding||c.4495_4496delTG|||||4328|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(PERM1|ENSG00000187642|3|0.67) GT:GS:BAF:LRR 0/0:0.7599:0:-0.10469136 1 1286108 rs555847974 CAA C . PASS ANN=C|frameshift_variant|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000325425.12|protein_coding|4/15|c.448_449delAA|p.Lys150fs|598/2679|448/2115|150/704||,C|frameshift_variant|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000338555.6|protein_coding|4/15|c.250_251delAA|p.Lys84fs|1394/3475|250/1917|84/638||,C|frameshift_variant|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000470022.1|protein_coding|4/4|c.358_359delAA|p.Lys120fs|586/645|358/417|120/138||WARNING_TRANSCRIPT_NO_STOP_CODON,C|frameshift_variant|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000379116.10|protein_coding|7/18|c.742_743delAA|p.Lys248fs|968/3050|742/2409|248/802||,C|frameshift_variant|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000400928.7|protein_coding|5/16|c.250_251delAA|p.Lys84fs|645/2731|250/1917|84/638||,C|upstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000379099.3|proteincoding||c.-1001-1000delAA|||||1000|WARNING_TRANSCRIPT_INCOMPLETE,C|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000467651.2|processed_transcript||n.512_513delAA|||||512|,C|non_coding_transcript_exon_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000379101.8|nonsense_mediated_decay|6/17|n.648_649delAA||||||;LOF=(SCNN1D|ENSG00000162572|8|0.63) GT:GS:BAF:LRR 0/0:0.4226:0:0.05689301 1 1287831 rs749990768 C T . PASS ANN=T|stop_gained|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000325425.12|protein_coding|8/15|c.1264C>T|p.Arg422|1414/2679|1264/2115|422/704||,T|stop_gained|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000338555.6|protein_coding|8/15|c.1066C>T|p.Arg356|2210/3475|1066/1917|356/638||,T|stop_gained|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000379116.10|protein_coding|11/18|c.1558C>T|p.Arg520|1784/3050|1558/2409|520/802||,T|stop_gained|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000400928.7|protein_coding|9/16|c.1066C>T|p.Arg356|1461/2731|1066/1917|356/638||,T|stop_gained|HIGH|SCNN1D|ENSG00000162572|transcript|ENST00000379099.3|protein_coding|2/7|c.514C>T|p.Arg172|515/923|514/922|172/306||WARNING_TRANSCRIPT_INCOMPLETE,T|3_prime_UTR_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000379101.8|nonsense_mediated_decay|10/17|n.477C>T|||||894|,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000354700.10|protein_coding||c.5733G>A|||||4560|,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|transcript|ENST00000492936.5|retained_intron||n.4559G>A|||||4559|,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000470022.1|protein_coding||c.1663C>T|||||1663|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000467651.2|processed_transcript||n.2234C>T|||||2234|,T|non_coding_transcript_exon_variant|MODIFIER|SCNN1D|ENSG00000162572|transcript|ENST00000379101.8|nonsense_mediated_decay|10/17|n.477C>T||||||;LOF=(SCNN1D|ENSG00000162572|8|0.63);NMD=(SCNN1D|ENSG00000162572|8|0.63) GT:GS:BAF:LRR 0/0:0.4606:0:0.051256247 1 1318875 rs62623580 G A . PASS ANN=A|stop_gained|HIGH|INTS11|ENSG00000127054|transcript|ENST00000429572.5|protein_coding|4/4|c.850C>T|p.Gln284|908/1104|850/870|284/289||,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000462432.5|processed_transcript||n.-1425C>T|||||1425|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000478641.5|retained_intron||n.-3705C>T|||||3705|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000531292.5|retained_intron||n.-4211C>T|||||4211|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000467408.6|retained_intron||n.-3274C>T|||||3274|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000533916.5|retained_intron||n.-3178C>T|||||3178|,A|upstream_gene_variant|MODIFIER|ENSG00000240731|ENSG00000240731|transcript|ENST00000444968.1|pseudogene||n.-186C>T|||||186|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000527383.5|nonsense_mediated_decay||n.-3269C>T|||||3267|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000531020.1|retained_intron||n.-3734C>T|||||3734|,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000470030.6|retained_intron||n.-3442C>T|||||3442|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000493534.6|processed_transcript||n.185C>T|||||185|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000532952.5|processed_transcript||n.472C>T|||||472|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000490853.5|processed_transcript||n.506C>T|||||506|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000534345.5|protein_coding||c.431C>T|||||431|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000531019.5|nonsense_mediated_decay||n.832C>T|||||506|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000498476.6|protein_coding||c.528C>T|||||528|WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000525285.1|nonsense_mediated_decay||n.1988C>T|||||1603|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000530233.1|retained_intron||n.3896C>T|||||3896|,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000470679.3|nonsense_mediated_decay||n.1013C>T|||||595|,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000323275.10|retained_intron|3/15|n.817+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000435064.6|protein_coding|4/16|c.429+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000540437.5|protein_coding|6/18|c.447+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000545578.5|protein_coding|5/17|c.342+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000620829.4|protein_coding|2/14|c.140-3261C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000421495.6|protein_coding|1/13|c.-529-3257C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000458452.7|nonsense_mediated_decay|6/18|n.713+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000419704.5|protein_coding|2/14|c.126+2121C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000527098.5|nonsense_mediated_decay|5/17|n.257+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000488042.6|retained_intron|4/6|n.450+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000525603.1|retained_intron|2/2|n.679+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000526797.5|nonsense_mediated_decay|4/6|n.92+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000526332.5|protein_coding|2/4|c.57+421C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000526904.5|retained_intron|1/1|n.79-3257C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000411962.5|protein_coding|2/14|c.136-3257C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000532772.5|nonsense_mediated_decay|2/12|n.126+2121C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000450926.6|protein_coding|4/16|c.429+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000528879.5|nonsense_mediated_decay|4/13|n.429+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000531377.5|nonsense_mediated_decay|1/6|n.51+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000434694.6|protein_coding|4/6|c.653+197C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000430786.5|nonsense_mediated_decay|6/8|n.307+421C>T||||||,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000527719.5|protein_coding|5/7|c.447+421C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000530031.5|protein_coding|5/7|c.570+421C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000526113.1|retained_intron|1/2|n.58-3257C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000498173.2|retained_intron|3/3|n.1395C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|transcript|ENST00000496353.1|retained_intron|2/2|n.2250C>T|||||| GT:GS:BAF:LRR 0/0:0.7443:0.0017591715:0.08530161 1 1338000 rs797044837 CT C . PASS ANN=C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378891.9|protein_coding|14/15|c.1615delA|p.Ser539fs|1662/2926|1615/2013|539/670||,C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378888.10|protein_coding|14/15|c.1690delA|p.Ser564fs|2043/3305|1690/2088|564/695||,C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000632445.1|protein_coding|4/6|c.619delA|p.Ser207fs|619/785|619/654|207/217||WARNING_TRANSCRIPT_NO_START_CODON,C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000631679.1|protein_coding|7/8|c.721delA|p.Ser241fs|721/778|721/756|241/251||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|transcript|ENST00000339381.6|protein_coding||c.3537delT|||||2687|,C|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000472445.1|retained_intron||n.3769delA|||||3769|,C|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000633096.1|retained_intron||n.1491delA|||||1491|,C|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000634054.1|retained_intron||n.333delA|||||333|,C|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|transcript|ENST00000616525.1|miRNA||n.1649delA|||||1649|;LOF=(DVL1|ENSG00000107404|7|0.43) GT:GS:BAF:LRR 0/0:0.3010:0.0060598357:-0.04165465 1 1338086 rs797044838 AC A . PASS ANN=A|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378891.9|protein_coding|14/15|c.1529delG|p.Gly510fs|1576/2926|1529/2013|510/670||,A|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378888.10|protein_coding|14/15|c.1604delG|p.Gly535fs|1957/3305|1604/2088|535/695||,A|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000632445.1|protein_coding|4/6|c.533delG|p.Gly178fs|533/785|533/654|178/217||WARNING_TRANSCRIPT_NO_START_CODON,A|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000631679.1|protein_coding|7/8|c.635delG|p.Gly212fs|635/778|635/756|212/251||WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|transcript|ENST00000339381.6|protein_coding||c.3623delC|||||2773|,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000472445.1|retained_intron||n.3683delG|||||3683|,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000633096.1|retained_intron||n.1405delG|||||1405|,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000634054.1|retained_intron||n.247delG|||||247|,A|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|transcript|ENST00000616525.1|miRNA||n.1563delG|||||1563|;LOF=(DVL1|ENSG00000107404|7|0.57) GT:GS:BAF:LRR 0/0:0.5086:0:-0.14043668 1 1338096 rs797044835 CA C . PASS ANN=C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378891.9|protein_coding|14/15|c.1519delT|p.Trp507fs|1566/2926|1519/2013|507/670||,C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378888.10|protein_coding|14/15|c.1594delT|p.Trp532fs|1947/3305|1594/2088|532/695||,C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000632445.1|protein_coding|4/6|c.523delT|p.Trp175fs|523/785|523/654|175/217||WARNING_TRANSCRIPT_NO_START_CODON,C|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000631679.1|protein_coding|7/8|c.625delT|p.Trp209fs|625/778|625/756|209/251||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|transcript|ENST00000339381.6|protein_coding||c.3633delA|||||2783|,C|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000472445.1|retained_intron||n.3673delT|||||3673|,C|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000633096.1|retained_intron||n.1395delT|||||1395|,C|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000634054.1|retained_intron||n.237delT|||||237|,C|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|transcript|ENST00000616525.1|miRNA||n.1553delT|||||1553|;LOF=(DVL1|ENSG00000107404|7|0.57) GT:GS:BAF:LRR 0/0:0.4713:0:0.2488735 1 1338098 rs797044834 GGGGGCAGCCGGGT G . PASS ANN=G|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378891.9|protein_coding|14/15|c.1505_1517delACCCGGCTGCCCC|p.His502fs|1564/2926|1505/2013|502/670||,G|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000378888.10|protein_coding|14/15|c.1580_1592delACCCGGCTGCCCC|p.His527fs|1945/3305|1580/2088|527/695||,G|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000632445.1|protein_coding|4/6|c.509_521delACCCGGCTGCCCC|p.His170fs|521/785|509/654|170/217||WARNING_TRANSCRIPT_NO_START_CODON,G|frameshift_variant|HIGH|DVL1|ENSG00000107404|transcript|ENST00000631679.1|protein_coding|7/8|c.611_623delACCCGGCTGCCCC|p.His204fs|623/778|611/756|204/251||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|transcript|ENST00000339381.6|protein_coding||c.3635_3647delGGGGCAGCCGGGT|||||2785|,G|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000472445.1|retained_intron||n.3659_3671delACCCGGCTGCCCC|||||3671|,G|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000633096.1|retained_intron||n.1381_1393delACCCGGCTGCCCC|||||1393|,G|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|transcript|ENST00000634054.1|retained_intron||n.223_235delACCCGGCTGCCCC|||||235|,G|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|transcript|ENST00000616525.1|miRNA||n.1539_*1551delACCCGGCTGCCCC|||||1551|;LOF=(DVL1|ENSG00000107404|7|0.57) GT:GS:BAF:LRR 0/0:0.3364:0:0.02459389

celine-weng commented 3 months ago

I realized that after I further filter my vcf file, I got no WARNING when I run the vep. Is this the problem with certain line in my original vcf files?

celine-weng commented 3 months ago

After further trials, I found out that only this line showing warning:

CHROM | POS | ID | REF | ALT | FORMAT | 202485320131_R03C01

-- | -- | -- | -- | -- | -- | -- 17 | 59169809 | 17:57247170 | C | CA | GT:GS:BAF:LRR | 0/0:0.3868:0.00657749:-0.0648169

celine-weng commented 3 months ago

I have found the problem is within our vcf file, not with the vep program, thank you!