The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Supplying a bed file to GATK haplotype caller
I tried to find this option but I was unsuccessful. I would like to call SNPs only on a subset of my bam files, that is only on specific chromosomes. I have now done so by getting a subset of bamfile, I was wondering if there is a way to provide Haplotype caller a bed file with the list of chromosomes I want for SNP calling in order to skip the subsetting step?