Picard's command line syntax is changing - Githubissues

sjanssen2 / spike

NGS pipeline for SNV detection in tumor context

BSD 3-Clause "New" or "Revised" License

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Picard's command line syntax is changing #239

Open deyazoubi opened 4 years ago

deyazoubi commented 4 years ago

NOTE: Picard's command line syntax is changing. For more information, please see:

https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) The command line looks like this in the new syntax:

FixMateInformation -INPUT /home/deya/Desktop/valiate_bam/KB0299_f.srt.bam -O fixed_mate.bam -ADD_MATE_CIGAR true

[ ] update Picard to new version
[ ] testing the tool