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samtools/bcftools: How to inspect SNPs not made it into vcf file

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  • samtools/bcftools: How to inspect SNPs not made it into vcf file

    Hi,

    Is there any parameter to "log" the snp-calling for individual SNP's which did not make it into the .vcf ? Or any other way to look how are the parameters for that SNP, if called ?

    Info: We generate our vcf's like this:

    samtools mpileup -ugf 'human_build37_ucsc.fa' 'test.bam' | bcftools view -bvcg - > 'test.bam.bcf'
    bcftools view 'test.bam.bcf' > 'test.bam.bcf.vcf'


    Thx,
    muenalan

  • #2
    I'm not sure if I understand your question correctly.

    In general, omitting the "-v" in bcftools will show you all positions, not just the variants.

    A convenient way to manually inspect a single position that didn't get called is the "samtools mpileup -r" option, where eg "samtools mpileup -r CHROMOSOMEII:10-10 ..." will show you only this one location.

    If you are talking about doing this in bulk for the whole genome, a possibility is to do a second pileup of all positions and then find the differences via "diff" or a custom script.

    Hope to help,

    best
    Andreas

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    • #3
      [solved]

      Yes,

      Exactly the information I was looking for.

      Thx,
      M!

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