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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?