Remove the mpileup BAM_CREF_SKIP filter.#2281
Open
jkbonfield wants to merge 1 commit intosamtools:developfrom
Open
Remove the mpileup BAM_CREF_SKIP filter.#2281jkbonfield wants to merge 1 commit intosamtools:developfrom
jkbonfield wants to merge 1 commit intosamtools:developfrom
Conversation
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
added a commit
to jkbonfield/bcftools
that referenced
this pull request
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
Contributor
Author
|
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. |
Member
|
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. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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