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Add picard command in the ConsensusCruncher.py #13

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arnavaz opened this issue Jan 15, 2020 · 0 comments

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arnavaz commented Jan 15, 2020

Is your feature request related to a problem? Please describe.

Removing the readgroup arguments in the bwa aligner command and add Picard AddReplaceReadgroups after the bam file is created.

Describe the solution you'd like
java -jar picard.jar AddOrReplaceReadGroups RGID=4
RGLB=lib1
RGPL=ILLUMINA
RGPU=unit1
RGSM=20

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

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