VarBen Manual
User Manual:
Open the PDF directly: View PDF
Page Count: 6
- Introduction
- Function 1. Mutation editor (muteditor.py)
- Function 2. SV/CNV editor (sveditor.py)
- Local optional arguments (only used in muteditor.py)
- Local optional arguments (only used in sveditor.py)
- Global optional arguments
- -h, --help
- -b BAMFILE, --bamfile BAMFILE
- -r REFFASTA, --reffasta REFFASTA
- -o OUTDIR, --outdir OUTDIR
- --alignerIndex ALIGNERINDEX
- -p PROCESS, --process PROCESS
- --seqer SEQER
- -g, --single
- --aligner ALIGNER
- --haplosize HAPLOSIZE
- --mindepth MINDEPTH
- --minmutreads MINMUTREADS
- --snpfrac SNPFRAC
- --minmapq MINMAPQ
- --multmapfilter
- --diffcover DIFFCOVER
- --floworder FLOWORDER
- --libkey LIBKEY
- --barcode BARCODE
- --tag
- -h, --help