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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Explicitly pass bam file to genotype #84

Closed b97pla closed 7 years ago

b97pla commented 7 years ago

This PR fixes an issue where the wrong bam file names were assumed for genotyping in the GenotypeConcordance check. This was due to bam files being wrapped inside GATKProcessingTargets and the genotyping method made assumptions of what file name to use for genotyping (the file resulting after processing). For the GenotypeConcordance check, genotyping is also done already on the raw alignments and this was not properly handled.

@johandahlberg, review and suggestions welcome. This has been tested on Milou, on chr22 of a CEPH sample using earlier pipeline-generated genotypes as the truth set.

johandahlberg commented 7 years ago

I think that this looks good, however I think it would be good if we could go over these changes together before I merge. Ping me and we can book a code review session.