error in mae

[Acetyl-ZHOU]

I run the mae,but have some problem. [W::hts_idx_load2] The index file is older than the data file: /Users/huizhou/Documents/1_allelic/drop_demo/qc_vcf_1000G_hg19.vcf.gz.tbi Error: BiocParallel errors 2 remote errors, element index: 1, 2 0 unevaluated and other errors first remote error: invalid class “ScanVcfParam” object: ScanVcfParam: 'geno' cannot be specified if 'samples' is 'NA' Execution halted can you give me some help?

[vyepez88]

Hi, it seems that there is something wrong with one of your vcf files or ids from the RNA BAM files. In which step exactly did this happen?

[Acetyl-ZHOU]

I want run snakemake --cores all sampleAnnotation mae and get that problem. My VCF and bam files also hg19. this is my config.yaml `projectTitle: "Detection of RNA Outliers Pipeline" root: /Users/huizhou/Documents/1_allelic/drop_demo/RNAdata/Output # root directory of all output objects and tables htmlOutputPath: /Users/huizhou/Documents/1_allelic/drop_demo/RNAdata/Output/html # path for HTML rendered reports indexWithFolderName: true # whether the root base name should be part of the index name

hpoFile: null # if null, downloads it from webserver sampleAnnotation: /Users/huizhou/Documents/1_allelic/drop_demo/RNAdata/sampleAnnotation.tsv # path to sample annotation (see documentation on how to create it)

geneAnnotation: v45: /Users/huizhou/Documents/1_allelic/drop_demo/gencode.v45lift37.basic.annotation.gtf genomeAssembly: hg19 genome: /Users/huizhou/Documents/1_allelic/drop_demo/hg19.fa

exportCounts:

specify which gene annotations to include and which

# groups to exclude when exporting counts
geneAnnotations:
    - v45
excludeGroups:
    - null

aberrantExpression: run: false groups:

• all fpkmCutoff: 1 implementation: autoencoder padjCutoff: 0.05 zScoreCutoff: 0 genesToTest: null maxTestedDimensionProportion: 3 yieldSize: 2000000

aberrantSplicing: run: false groups:

• all recount: false longRead: false keepNonStandardChrs: false filter: true minExpressionInOneSample: 20 quantileMinExpression: 10 minDeltaPsi: 0.05 implementation: PCA padjCutoff: 0.1 maxTestedDimensionProportion: 6 genesToTest: null

  FRASER1 configuration

  FRASER_version: "FRASER" deltaPsiCutoff : 0.3 quantileForFiltering: 0.95

mae: run: true groups:

• all gatkIgnoreHeaderCheck: true padjCutoff: 0.05 allelicRatioCutoff: 0.8 addAF: true maxAF: 0.001 maxVarFreqCohort: 0.05

  VCF-BAM matching

  qcVcf: /Users/huizhou/Documents/1_allelic/drop_demo/qc_vcf_1000G_hg19.vcf.gz qcGroups:

  • all dnaRnaMatchCutoff: 0.85

rnaVariantCalling: run: true groups:

• all highQualityVCFs:
• /Users/huizhou/Documents/1_allelic/drop_demo/Mills_and_1000G_gold_standard.indels.hg19.sites.chrPrefix.vcf.gz
• /Users/huizhou/Documents/1_allelic/drop_demo/1000G_phase1.snps.high_confidence.hg19.sites.chrPrefix.vcf.gz dbSNP: /Users/huizhou/Documents/1_allelic/drop_demo/00-All.vcf.gz repeat_mask: /Users/huizhou/Documents/1_allelic/drop_demo/hg19_repeatMasker_sorted.chrPrefix.bed createSingleVCF: true addAF: true maxAF: 0.001 maxVarFreqCohort: 0.05 hcArgs: "" minAlt: 3 yieldSize: 100000

tools: gatkCmd: gatk bcftoolsCmd: bcftools samtoolsCmd: samtools`

[Acetyl-ZHOU]

I also find some problem with this. [W::vcf_parse_filter] FILTER 'VarFreq,VarMapQual,MinMMQSdiff' is not defined in the header [E::bcf_hdr_parse_line] Could not parse the header line: "##FILTER=<ID=VarFreq,VarMapQual,MinMMQSdiff,Description=\"Dummy\">" [E::vcf_parse_filter] Could not add dummy header for FILTER 'VarFreq,VarMapQual,MinMMQSdiff' at chr1:10048 [W::vcf_parse_filter] FILTER 'NoReadCounts' is not defined in the header [W::vcf_parse_filter] FILTER 'MinMMQSdiff' is not defined in the header

what I can do with header?

[vyepez88]

Hi, be sure to double-check your vcf files format, for example:

• it should contain a column with the sample name containing the genotype of that sample. That sample name is what you should specify in the DNA_ID column of the sample annotation
• the header contains all the values present in the FILTER, INFO and FORMAT columns

[Acetyl-ZHOU]

In my DNA VCF file the header is like this. ##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases wit h Phred score >= 15"> 4 ##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wi ld-type)"> 5 ##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous -variant"> 6 ##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-v ariant"> 7 ##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> 8 ##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting re ads on one strand"> 9 ##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this positio n"> 10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 11 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 12 ##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMto ols"> 13 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phr ed score >= 15"> 14 ##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> 15 ##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (r eads2)"> 16 ##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> 17 ##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test" 24 ##FILTER=<ID=VarCount,Description="Fewer than 4 variant-supporting reads"> 25 ##FILTER=<ID=VarFreq,Description="Variant allele frequency below 0.05"> 26 ##FILTER=<ID=VarReadPos,Description="Relative average read position < 0.01"> 27 ##FILTER=<ID=VarDist3,Description="Average distance to effective 3' end < 0.01"> 28 ##FILTER=<ID=VarMMQS,Description="Average mismatch quality sum for variant reads > 100" > 29 ##FILTER=<ID=VarMapQual,Description="Average mapping quality of variant reads < 15"> 30 ##FILTER=<ID=VarBaseQual,Description="Average base quality of variant reads < 28"> 31 ##FILTER=<ID=Strand,Description="Strand representation of variant reads < 0.01"> 32 ##FILTER=<ID=RefMapQual,Description="Average mapping quality of reference reads < 15"> 33 ##FILTER=<ID=RefBaseQual,Description="Average base quality of reference reads < 28"> 34 ##FILTER=<ID=MMQSdiff,Description="Mismatch quality sum difference (ref - var) > 50"> 35 ##FILTER=<ID=MapQualDiff,Description="Mapping quality difference (ref - var) > 50"> 36 ##FILTER=<ID=ReadLenDiff,Description="Average supporting read length difference (ref - var) > 0.25">

do I need to add this information to sample annotaion? Or change vcf file?

[vyepez88]

it seems that MinMMQSdiff is not defined in the VCF file header. You would need to modify your VCF files.

[Acetyl-ZHOU]

So can I just write something for MinMMQSdiff? I don`t know how to add this to my Vcf.

[vyepez88]

consider validating your vcf files beforehand using for example the validation on only VCF format tests from GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360037057272-ValidateVariants