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DKFZ-ODCF / AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs
https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows/wiki
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Use bwa-postalt.js postprocessing for alignment against hg38 with ALT contigs #79

Closed vinjana closed 2 years ago

vinjana commented 2 years ago

bwa-postalt.js support.

Tested with few BAMs, running with and without bwa-postalt.js. The BAMs created with bwa-postalt.js contained "om" tags (is this original MAPQ -- not documented anywhere :-( ).

The configuration changes related to the tbi-lsf-cluster.sh script are kind of provisional, because there is no bwakit installation yet in our cluster.

vinjana commented 2 years ago

This looks good @vinjana The BWA version should be checked for alt-aware alignments, or for the GRCh38 alignments, the default BWA should be >=0.7.14

According to the BWA README, version 0.7.11 is the first version. This is what I added as comment to the description of the runBwaPostAlt option in the XML.

NagaComBio commented 2 years ago

So, the prefix should be set to the correct path, then. Something like $outputDir/hla_file?

Yes, this will work. The file will contain all the reads mapped to the HLA alleles. For the WGS, it should be less than 5GB.

vinjana commented 2 years ago

O.k. Merging it.

vinjana commented 2 years ago

Thanks, @NagaComBio for reviewing and testing!