Hello all,
I was setting up my human exome sequencing analysis pipeline mostly according to the How-to/exome analysis manual. My question is in the producing raw SNP call step using UnifiedGenotyper. From the best practises on GATK web site I know that it is better to give multiple BAM files to UnifiedGenotyper at the same time and output one multi sample VCF file. However, my impression from the How-to and other exome pipelines is that giving one file to UnifiedGenotyper each time to obtain one single sample VCF file is more common. And I also find it is easier to manage the different files when I have one VCF file for each individual. I did a comparison of the two methods and number of obtained SNPs are different. So what is the benefit of calling variants using UnifiedGenotyper with multiple BAM files?
I was setting up my human exome sequencing analysis pipeline mostly according to the How-to/exome analysis manual. My question is in the producing raw SNP call step using UnifiedGenotyper. From the best practises on GATK web site I know that it is better to give multiple BAM files to UnifiedGenotyper at the same time and output one multi sample VCF file. However, my impression from the How-to and other exome pipelines is that giving one file to UnifiedGenotyper each time to obtain one single sample VCF file is more common. And I also find it is easier to manage the different files when I have one VCF file for each individual. I did a comparison of the two methods and number of obtained SNPs are different. So what is the benefit of calling variants using UnifiedGenotyper with multiple BAM files?
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