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  • Allelic Depth from VCF

    I'm trying to estimate the # of reads representing each allele across multiple samples in RNA-seq data.

    I've identified SNPs with samtools mpileup and vcftools call, but allelic depth is not provided in the vcf.

    I gather that GATK Variant Annotator (-A DepthPerAlleleBySample) might be able to extract this info from the vcf, but GATK seems unhappy with my vcf format

    Code:
    Your input file has a malformed header: unexpected tag count 5 in line <ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
    Does anyone have other suggests for getting per sample/per allele counts? Or a suggestion to get around this formatting issue?

    Thanks!

  • #2
    I seem to remember that with bcftools, you can have this information in the bcf file...

    Comment


    • #3
      OOps, I meant "bcftools call" not vcftools

      Comment


      • #4
        If you pass the DPR option to bcftools call it gives the allele depth (I also do DP for total read depth):
        samtools mpileup -gu -t DP,DPR

        The output is 0/1:153,0,125:61:20,41,0,0
        0/1 allele call
        153,0,125 prob of allele call
        61 read depth
        20,41,0,0 depth of different alleles
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

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        • #5
          Allelic Depth

          Excellent! I'll give it a shot!

          Comment

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