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

[AtaJadidAhari]

Hey @Acetyl-ZHOU, any updates on the issue?