is it reasonable to use splitted bam per chr to run mutect

for running mutect for whole genome sequencing data is pretty time-consuming, is it reasonable to first split bam file into per-chromosome-based smaller ones and then run mutect against per-chr bam file?

i am not quite sure whether mutect will use some cross chromosome information.

Answers

  • pruzanovpruzanov Member

    @liuxq_shishui said:
    for running mutect for whole genome sequencing data is pretty time-consuming, is it reasonable to first split bam file into per-chromosome-based smaller ones and then run mutect against per-chr bam file?

    I would rather use the whole .bam with --intervals parameter, i.e. --intervals chr4:1-191154276 (for chromosome 4 in hg19) This way you may produce result files (one set per chromosome) and analyze them separately, or in case of .vcf output merge them with vcftools

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