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Samtools version 1.0.7 and 1.0.10 different pileup

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  • Samtools version 1.0.7 and 1.0.10 different pileup

    Hi

    When I run pileup in samtools (samtools pileup -f ref.fa input.bam > results.pileup) I get considerably less reads when using v1.0.10 than 1.0.7. For example I have a 6kb amplicon - every base has ~30% fewer reads in .0.10. The bam and ref are the same. Does the later version of samtools filter reads??

  • #2
    Originally posted by mrxcm3 View Post
    Hi

    When I run pileup in samtools (samtools pileup -f ref.fa input.bam > results.pileup) I get considerably less reads when using v1.0.10 than 1.0.7. For example I have a 6kb amplicon - every base has ~30% fewer reads in .0.10. The bam and ref are the same. Does the later version of samtools filter reads??
    A good place to start would be to email the samtools help list:
    [email protected]

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