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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
The text was updated successfully, but these errors were encountered:
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?
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
The text was updated successfully, but these errors were encountered: