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Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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newer picard versions have "too many file open" issues with demultiplexing #19

Open Kurt-Hetrick opened 1 year ago

Kurt-Hetrick commented 1 year ago

ran into a problem when converting into unmapped bam files. need to investigate eventually, but for now will have to create a container using picard version that brian was using.

https://github.com/broadinstitute/picard/issues/1714

Kurt-Hetrick commented 8 months ago

use SORT=false this worked for IlluminaBaseCallsToSam, but I have to look into ExtractIlluminaBarcodes. I think new versions were having issues and I had to revert back to 2.17 to get it to work for the novaseqx

Kurt-Hetrick commented 8 months ago

also old versions of picard are not immune to having too many file handles open (hence why i had to use SORT=false)