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  • samtools indels

    Hi everyone,
    I have a problem calling indels with samtools. Up to now, I called variants with the following command:
    samtools pileup -vcf ref.fasta mapping.bam > raw_variants.var
    and created the pileup file with:
    samtools pileup -cf ref.fasta mapping.bam > mapping.pileup
    After that I added the filter steps. But for my last samples I didn't receive any indels (just SNPs). In the mapping I can see indels, but neither in the pileup-file nor in the variance-files are indels. Are there any parameter to include/exclude indels? Or do I have to do anything different for Solid-reads mapped with Bioscope in comparision to Illumina-reads?

    Thanks for your help!

  • #2
    Have you thought about updating to the newer version of SAMtools that uses mpileup instead of pileup?

    Comment


    • #3
      I tried with mpileup as well, but also in that file I can't see the indels

      Comment


      • #4
        Try these commands:

        samtools-0.1.18/samtools mpileup -AB -ugf <reference_sequence> <aligned_file> | samtools-0.1.18/bcftools/bcftools view -bvcg -> <intermediate_file>

        samtools-0.1.18/bcftools/bcftools view -e <intermediate_file> | samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > <variants.txt>

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