usage: chisel-pseudonormal.py [-h] -r REFERENCE [-x RUNDIR] [-e THRESHOLD]
[-b SIZE] [-c CHROMOSOMES] [-m MINREADS]
[--samtools SAMTOOLS] [-j JOBS]
[--tmpdir TMPDIR] [-n NORMAL]
INPUT
CHISEL command to generate a pseudo-matched normal sample by extracting
diploid cells from a barcoded single-cell BAM file.
positional arguments:
INPUT Barcoded single-cell BAM file
optional arguments:
-h, --help show this help message and exit
-r REFERENCE, --reference REFERENCE
Reference genome
-x RUNDIR, --rundir RUNDIR
Running directory (default: current directory)
-e THRESHOLD, --threshold THRESHOLD
Minimum fraction of diploid genome to select diploid
cells (default: 0.9)
-b SIZE, --size SIZE Bin size, with or without "kb" or "Mb"
-c CHROMOSOMES, --chromosomes CHROMOSOMES
Space-separeted list of chromosomes between apices
(default: "chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8
chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17
chr18 chr19 chr20 chr21 chr22")
-m MINREADS, --minreads MINREADS
Minimum number total reads to select cells (default:
100000)
--samtools SAMTOOLS Path to the directory to "samtools" executable,
required in default mode (default: samtools is
directly called as it is in user $PATH)
-j JOBS, --jobs JOBS Number of parallele jobs to use (default: equal to
number of available processors)
--tmpdir TMPDIR Temporary directory in running directory (default:
_TMP)
-n NORMAL, --normal NORMAL
Name of the generated pseudo matched-normal BAM file
(default: pseudonormal.bam)