a) used version: gatk-18.104.22.168
b) used command:
I pooled many individuals of plant into a pool and add a mutant with known mutation site (191 wild type DNA and 1mutant), I used HaplotypeCaller to call SNP, but gvcf file and vcf file are both don't have the known mutation site. And I used IGVtools to check the bam file before call snp with HaplotypeCaller, I can find the known alternative base at the target site. So why the bam file have the known mutation but HaplotypeCaller can't input this. I don't know how to change the parameters (I tried -stand-call-conf --minimum-mapping-quality -mbq).
By the way, I used bcftools to call snp and I can find the known mutation site in vcf files, so I think maybe the filters of HaplotypeCaller are so strict with snp?
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