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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Indel Realignment and Alignment Metadata #6459

Closed DarioS closed 4 years ago

DarioS commented 4 years ago

In the news file of a structural variant software I use, I read

Added FIX_SA and FIX_MISSING_HARD_CLIP FIX_SA: rewrites split read SA tags corrects GATK indel realignment SA tag data inconsistency FIX_MISSING_HARD_CLIP: infers missing hard clipping if split read records have different lengths corrects for GATK indel realignment stripping hard clipping when realigning

Could such issues perhaps be resolved in an update to GATK?

ldgauthier commented 4 years ago

Those sound like issues with the IndelRealigner tool from GATK3, which is not part of our pipeline anymore. Is this still a problem with 4.1.4.1?

On Wed, Feb 19, 2020, 1:00 AM Dario Strbenac notifications@github.com wrote:

In the news file of a structural variant software I use, I read

Added FIX_SA and FIX_MISSING_HARD_CLIP FIX_SA: rewrites split read SA tags corrects GATK indel realignment SA tag data inconsistency FIX_MISSING_HARD_CLIP: infers missing hard clipping if split read records have different lengths corrects for GATK indel realignment stripping hard clipping when realigning

Could such issues perhaps be resolved in an update to GATK?

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DarioS commented 4 years ago

Indeed, this is no longer a problem with GATK4.