PostprocessGermlineCNVCalls does not report QUAL in output vcf for cnv
REQUIRED for all errors and issues:
a) GATK version used: gatk docker 4.1.3.0
b) Exact command used:
./gatk PostprocessGermlineCNVCalls --model-shard-path ./cohort500/cohort500_0001_of_11-model --calls-shard-path ./case-Test-vs-cohort500/case-Test-vs-cohort500_0001_of_11-calls --allosomal-contig chrX --allosomal-contig chrY --contig-ploidy-calls ploidy-Test-calls --sample-index 0 --output-genotyped-intervals ./outputs/Test/genotyped-intervals-Test-cohort500.vcf.gz --output-genotyped-segments ./outputs/Test/genotyped-segments-Test-cohort500.vcf.gz --sequence-dictionary ./reference/allchr.dict --output-denoised-copy-ratios Test_denoised_copy_ratios.tsv
c) Entire program log: no error reported.
In the docker of gatk (version 4.1.3.0) when we run germline cnv caller, and using PostprocessGermlineCNVCalls module for reporting flags, the output vcf missed the QUAL , and report "." for all reported cnv. What is the problem?
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Hi Damoun Nash
Can you provide an example output here that we can check?
Also did you provide all shards to PostprocessGermlineCNVCalls at the same time to process all the CNV information?
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Dear Gokalp,
yes, I send all shards for it, this is output example:
##source=PostprocessGermlineCNVCalls
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Test
chr1 68841 CNV_chr1_68841_70258 N <DEL>,<DUP> . . END=70258 GT:CN:NP:QA:QS:QSE:QSS 2:3:1:2:2:2:2
chr1 861072 CNV_chr1_861072_1414738 N <DEL>,<DUP> . . END=1414738 GT:CN:NP:QA:QS:QSE:QSS 0:2:322:7:905:12:7
chr1 1415997 CNV_chr1_1415997_1460921 N <DEL>,<DUP> . . END=1460921 GT:CN:NP:QA:QS:QSE:QSS 2:3:25:3:14:2:10
chr1 1461591 CNV_chr1_1461591_1567921 N <DEL>,<DUP> . . END=1567921 GT:CN:NP:QA:QS:QSE:QSS 0:2:38:7:131:12:2
We construct cohort via previous version of the CNVcaller of gatk, is it possible that this issue might be because of the version incompatibility?
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Hi Damoun Nash
This behavior belongs to versions prior to 4.1.5.0. Earlier versions of gCNV workflow only encoded QUAL values to FORMAT/QS tag and a later PR changed this behavior to add QUAL to also QUAL field.
https://github.com/broadinstitute/gatk/pull/6352
Our recommendation would be to use the latest GATK 4.6.0.0 for your analysis.
Regards.
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many thanks,
does its docker available (with GATK of version 4.6.0.0)?
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Hi again.
Yes we have prebuilt docker images for every release and nightly all of which can be found at the repositories below.
https://hub.docker.com/r/broadinstitute/gatk/tags
https://hub.docker.com/r/broadinstitute/gatk-nightly/tags
Regards.
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