I performed whole exome analysis using GATK pipeline. After annotation of variant using annovar, I performed these steps:
Filtered variants that have passed all filters Using Gnomad_exome_all, looked for variants less than 0.01
Then tried to confirm if these variants are also present in bam files in igv. Some of the variants which were heterozygous in the bam file were called as homozygous in jointcalled vcf file.
Why does this happen?. Can someone share their experience
Please sign in to leave a comment.