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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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alt allels error #8953

Open gaochenx opened 3 months ago

gaochenx commented 3 months ago

Instructions

gatk --java-options "-Xmx256g -XX:ParallelGCThreads=10" GenotypeGVCFs -R ./Zm_Mo17.fa -stand-call-conf 0 -ploidy 1 -V gendb:///share/home/gaochenxu/01.prj/50.pan-maize/2.sv/pan/03.vcf/gatk10 -O ./gatk10.vcf.gz --cloud-prefetch-buffer 10000 --cloud-index-prefetch-buffer 10000 --genomicsdb-max-alternate-alleles 110 --max-alternate-alleles 100 --gcs-max-retries 1000

Bug Report

Hello, when I was using GATK GenotypeGVCFs function call variant, I found that the result could be more than 3 alleles in alt. However, none of the samples in the generated vcf had genotypes other than 012

Expected behavior

alt genotype, there should be corresponding sample support

Actual behavior

But in fact, all the samples have only genotype 0/0 1/1 2/2, and no genotype 3/3 or above

So I was wondering, is there a problem with where I set it up

gokalpcelik commented 3 months ago

When ploidy is set to 1 none of your samples should have GTs with 0/0 1/1 2/2. Are you sure that your original VCF calls are made with ploidy 1 as well?