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  • samtools mpileup possible bug

    Hello,

    I noticed that last sample (last 3 columns) in mpileup format behave strangely in positions with low base quality (< 13). It looks like:

    0

    where it should be:

    0 * *

    Does anyone have similar issue? Is this a bug?

    It confuses my downstream scripts, because there are fewer columns in those positions than expected.

    I am using Version: 1.2 (using htslib 1.2.1)

  • #2
    It's a longstanding "feature" of samtools mpileup when coverage is 0 because of excluded bases rather than no mapped reads. I would imagine by now there are many scripts that check for this case and they might break if the mpileup were changed. I would simply modify your script to handle this case.

    Comment


    • #3
      Originally posted by dgscofield View Post
      It's a longstanding "feature" of samtools mpileup when coverage is 0 because of excluded bases rather than no mapped reads. I would imagine by now there are many scripts that check for this case and they might break if the mpileup were changed. I would simply modify your script to handle this case.
      I see, would you happen to know if this "feature" occurs only in last individual, or in your experience - it can occur anywhere? Many thanks for your reply!

      Comment


      • #4
        i believe it can occur anywhere, and i think you may find that the columns may be empty, but their positions are still delimited with tabs. so that instead of

        ... <tab> 0 <tab> * <tab> * <tab> ...

        it is

        .... <tab> 0 <tab> <tab> <tab> ...

        There is an additional wrinkle if you use the -s flag to include a read mapping quality column in the mpileup. In the case of "0 * *" entries, they are always three columns rather than the expected 4, while the "0 blank blank" entries are the expected four columns "0 blank blank blank".

        Comment


        • #5
          The additional -s wrinkle has been fixed since samtools 1.0.

          Thanks for the reminder to revisit the main problem reported here.

          Comment

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