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  • SNP calling using GATK UnifiedGenotyper

    Hi All
    I am trying to call SNPs/InDels in one of my BAM file using GATK UnifiedGenotyper. I am only interested in calling SNPs/InDels at randon positions (not all) specified by me. For example, at chromosome position-317, 34179, 57205, 82043 etc. I know that there is a -L option in UnifiedGenotyper, but I am not sure how to format my list of positions for this. Alternatively, I can call SNPs/InDels at all positions and then parse out the positions I want, but the genome size in my study is big and I just want to save some time.

    Appreciate your help

    Baika

  • #2
    YOu can try using BEDTools. You can filter the .bam for reads that intersect with a .bed file of target locations. That'll make downstream stuff lots simpler.

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