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  • find all snps/indels

    is there a good way to find all the snps and indels (or just deletions in the read) from a sam file? has anyone written an MD tag parser that can do this? i tried a workaround by using the samtools variant caller, but that filters a lot of the snps out from my sam file -- i can't get it to output every single snp and indel. any ideas?

  • #2
    samtools and GATK, as just two examples, will parse .bam files, and output variants.

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    • #3
      but they seem to filter variants. how do i completely turn the filter off and output every single variant present in the sam file?

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