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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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use sambamba for markduplicates #150

Closed alexg9010 closed 4 years ago

alexg9010 commented 4 years ago

compatible to picard: https://lomereiter.github.io/sambamba/docs/sambamba-markdup.html direct sorting : https://github.com/biod/sambamba/issues/183

alexg9010 commented 4 years ago

somehow only two files can be processed in parallel ... have to investigate this

alexg9010 commented 4 years ago

sambamba markdup has too many problems right now that require too much run-specific debugging https://github.com/biod/sambamba/issues/229 https://github.com/biod/sambamba/issues/189

alexg9010 commented 4 years ago

Will use samblaster instead.

alexg9010 commented 4 years ago

addresses https://github.com/BIMSBbioinfo/pigx_bsseq/issues/153 too