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  • indels from samtools

    I got a indel as following :
    chr1 7096787 . C CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 48.5 . INDEL;DP=35;AF1=0.501;CI95=0.5,0.5;DP4=1,0,2,6;MQ=57;FQ=-10.9;PV4=0.33,0.14,0.37,0.13 GT:PL:GQ 0/1:86,0,24:27

    above file is vcf formart. Does anybody know 'N' in fifth column?

    variant calling commnads are the follwing :

    samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
    bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

  • #2
    I'm not sure if you are asking for a deeper reason about why you have the Ns. But, in general, sequencing nomenclature N could be A/T/G/C.

    Comment


    • #3
      The N's means that the software isn't sure what those letters are, it just thinks there is something inserted there.

      I'd try a de novo assembler, see if that can work out what the sequence is in that region. With only 8 decent quality reads showing the insertion, I'd be skeptical.

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