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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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write a generalized demuxing pipeline for novaseqx #135

Open Kurt-Hetrick opened 6 months ago

Kurt-Hetrick commented 6 months ago
  1. should probably only need illumina experiment manager samplesheet (umi pipline uses cidr ss to grab lanes in addition to iem ss)
  2. said sample sheet will need to have a sample name field if it already does not have one
  3. question of whether to rev comp index 2 or not (possible flag)
  4. write out fastq (paired)
  5. make available MAX_MISMATCH (default 1)
  6. make available MAX_NO_CALLS (default 2)
  7. make available MIN_MISMATCH_DELTA (default 1)
  8. summarize barcodes seen per lane (top x number)
  9. collate per lane barcode metrics reports into one report per flowcell (submission)
  10. probably would be best to write this into a separate fastq folder and write fastq finding logic in bwa step for fastq files generated in this manner...even though unmapped bams can be used as an input into alignment, have to think about fastq files being a preferred deliverable.