Remove the mpileup BAM_CREF_SKIP filter. #2281
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Mpileup removes alignments using the cigar ref skip operator ("N").
This was originally added in 2011 in samtools/samtools#d1643d6 with
the commit message of "fixed a bug in indel calling related to
unmapped and refskip reads".
Unfortunately I don't know what that bug was, but removing the code
shows it still works (at least for some data!). We need better
understanding of what's going on and why it was added, so perhaps we
should add a command line option to control this instead?
Fixes samtools#2277
jkbonfield
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Sep 17, 2024
Mpileup removes alignments using the cigar ref skip operator ("N").
This was originally added in 2011 in samtools/samtools#d1643d6 with
the commit message of "fixed a bug in indel calling related to
unmapped and refskip reads".
Unfortunately I don't know what that bug was, but removing the code
shows it still works (at least for some data!). We need better
understanding of what's going on and why it was added, but this PR
makes it optional, keeping the default as before. Note there appears
to be no filtering of BAM_CREF_SKIP in indels-2.0 so the option would
be a nop there.
This is an alternative PR to samtools#2281. I've leave it to the project
maintainer as to what is preferable: removing the (no longer needed?)
filtering, or keeping the default behaviour identical and adding a new
option instead (which is safer, but possibly leads to accidental bad
calls due to not noticing a new option has appeared).
Fixes samtools#2277
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See also #2282 as an alternative to this PR. That is probably the way to go for compatibility, but then again I doubt anyone is currently using bcftools on RNASeq data with ref-skip based alignments given all such alignments were simply discarded, so it's unlikely the change in behaviour would break any currently working pipelines. |
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I believe the edited BAM_CREF_SKIP checking code Lines 855 to 859 in ef8b974 If we should merge any version of this, we'd need to include a small test to demonstrate where it can be helpful. |
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Mpileup removes alignments using the cigar ref skip operator ("N"). This was originally added in 2011 in samtools/samtools#d1643d6 with the commit message of "fixed a bug in indel calling related to unmapped and refskip reads".
Unfortunately I don't know what that bug was, but removing the code shows it still works (at least for some data!). We need better understanding of what's going on and why it was added, so perhaps we should add a command line option to control this instead?
Fixes #2277