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  • allele information from samtools mpileup contents

    Dear all,

    I need help with allele information from samtools mpileup contents

    I have the following workflow for diagnostics:

    samtools view -b whole_exome.sorted.bam chr2:12345678-32345678 > zoom_region.bam
    samtools mpileup -f ref.fa -B -q 1 -Q 30 -SD zoom_region.bam > info.mpileup.txt

    The subsequent info.mpileup.txt has information as described in


    Is there a script or automated method that can parse the allele info: #A, T, G, C .. from the mpileup / pileup information of the original bam file. I need to repeat this for many base positions, hence the need to automate it. Hope you can please help. Would appreciate any help / pointers.

    Thanks in advance,
    Best,
    sarosh

  • #2
    dear Sarosh,

    did you manage to get the per base ACGT count in any way?

    best,

    Dave

    Comment


    • #3
      Why not use bcftools to make a vcf, instead of a pileup file?

      Then if you want, filter the vcf with bedtools and a bedfile of your candidate regions.

      Comment

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