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[feature request] MergeBamAlignment: when merging from GRCh38 alignments, retain `AH:*` tag that notes which contigs were ALT-handled #625

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sooheelee opened this issue Aug 10, 2016 · 5 comments

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@sooheelee
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@sooheelee sooheelee commented Aug 10, 2016

This tag is overwritten during merging by MergeBamAlignment but would be a good idea to retain.

It is in the header @SQ lines and denotes if a contig was ALT-handled by BWA-MEM when aligning to GRCh38.

See Tutorial#8017's section 3. Specifically, look at the section titled How can I tell if a BAM was aligned with ALT-handling? to see example screenshots of what the AH tag looks like.

@yfarjoun

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@yfarjoun yfarjoun commented Aug 10, 2016

good point soohee!! thanks for figuring this out. I was wondering why the
AH:* tags are missing.

On Wed, Aug 10, 2016 at 1:02 PM, sooheelee notifications@github.com wrote:

This tag is overwritten during merging by MergeBamAlignment but would be a
good idea to retain.

It is in the header @sq lines and denotes if a contig was ALT-handled by
BWA-MEM when aligning to GRCh38.

See Tutorial#8017
http://gatkforums.broadinstitute.org/gatk/discussion/8017's section 3
http://gatkforums.broadinstitute.org/gatk/discussion/8017#3.
Specifically, look at the section titled How can I tell if a BAM was
aligned with ALT-handling?
to see example screenshots of what the AH tag
looks like.


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@yfarjoun yfarjoun commented Aug 11, 2016

@tfenne @nh13 @ktibbett The problem is that MBA takes the dictionary from the input reference file (or rather the nearby dictionary file).

I would like to propose to take it from the input aligned files instead. Do you see a problem with this idea for a fix?

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@tfenne tfenne commented Aug 12, 2016

@yfarjoun I think that will create problems unfortunately. Unless bwa is pulling through the other fields that are in the dictionary, which seems unlikely. The resulting BAMs would likely have @SQ lines that lost their MD, AS and UR tags, which would kinda suck. Maybe the thing to do is to merge the sequence dictionaries and take the union of tags between them?

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@yfarjoun yfarjoun commented Aug 12, 2016

Totally suck. Yes. it seems that bwa only picks up LN....OK. merging the
tags. Thanks for the comment.

On Fri, Aug 12, 2016 at 11:23 AM, Tim Fennell notifications@github.com
wrote:

@yfarjoun https://github.com/yfarjoun I think that will create problems
unfortunately. Unless bwa is pulling through the other fields that are in
the dictionary, which seems unlikely. The resulting BAMs would likely have
@sq lines that lost their MD, AS and UR tags, which would kinda suck.
Maybe the thing to do is to merge the sequence dictionaries and take the
union of tags between them?


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@yfarjoun yfarjoun commented Jan 17, 2017

will be fixed by #682

@yfarjoun yfarjoun closed this in afb4af3 Jan 17, 2017
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