Closed rhshah closed 5 years ago
org.mskcc.marianas.umi.duplex.DuplexUMIBamToCollapsedFastqSecondPass standard-bam-file pileup-file minMappingQuality minBaseQuality mismatches wobble minConsensusPercent reference-fasta-file first-pass.mate-position-sorted.txt
This will produce collapsed_R1_.fastq and collapsed_R2_.fastq files along with some QC files.
collapsed_R1_.fastq
collapsed_R2_.fastq
QC files.
we can probably close this now 💯
org.mskcc.marianas.umi.duplex.DuplexUMIBamToCollapsedFastqSecondPass standard-bam-file pileup-file minMappingQuality minBaseQuality mismatches wobble minConsensusPercent reference-fasta-file first-pass.mate-position-sorted.txt
This will produce
collapsed_R1_.fastq
andcollapsed_R2_.fastq
files along with someQC files.