I used GATK for the very fist time for a whole genome sequencing data in a pig line. I am seeing way too many SNPs and INDELS.
I used Haplotype Caller to generate gVCF files and Combine for merging all gVCFs. Then I used Joint Genotype call and got my final VCF.
I did try the VariantFiltration on my files and it didn't give me an error but the issue is still there.
Also, when there is joint genotype calling, shouldn't it be going for a SNP that is in 30% of samples instead??
Anyone who have figured a better way for non-human genome data, please do let me know.
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