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  • No output from Samtools pileup

    I tried to call consensus using samtools pileup from the filtered BAM file which has only reads with no mate. But the result was empty. The following is what I did:

    1) From the complete BAM, I extracted reads (mapQV >8) which have no mate (mate unmapped) using "samtools view -f 0x8" - There are ~35m reads.
    2) removed all duplicate reads using Picard
    3) provided this filtered file to samtools for consensus calling with options "-c", "-Q 8", "-f ref.fas" ( i tried -m, -M as well)

    Question here is 1) Why does pileup fail to call consensus 2) Did i make any mistake or do I modify any parameters 3) Is there any other tool can do this?

    Any light to this will be a great help.

    Thanks.

    Praveen

  • #2
    Some tests I just did show that samtools mpileup only works for proper pairs. Can anyone else confirm this?

    I was not able to call any variants until I marked the pairs with bamtools resolve.

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