NAME
alleleCounter - NGS copy number algorithms
SYNOPSIS
alleleCounter -l loci_file.txt -b sample.bam -o output.txt [-m int] [-r ref.fa.fai]
DESCRIPTION
Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings).
OPTIONS
- -l --loci-file [file]
-
Path to loci file.
- -b --hts-file [file]
-
Path to sample HTS file.
- -o --output-file [file]
-
Path write output file.
Optional
- -r --ref-file [file]
-
Path to reference fasta index file. NB. If cram format is supplied via -b and the reference listed in the cram header
-
can't be found alleleCounter may fail to work correctly.
- -m --min-base-qual [int]
-
Minimum base quality [Default: 20].
- -q --min-map-qual [int]
-
Minimum mapping quality [Default: 35].
- -c --contig [string]
-
Limit calling to named contig.
- -d --dense-snps
-
Improves performance where many positions are close together
- -x --is-10x
-
Enables 10X processing mode. In this mode the HTS input file must be a cellranger produced BAM file. Allele counts are then given on a per-cellular barcode basis, with each count representing the consensus base for that UMI.
-
by iterating through bam file rather than using a 'fetch' approach.
- -f --required-flag [int]
-
Flag value of reads to retain in allele counting default: [3]. N.B. if the proper-pair flag is are selected, alleleCounter will assume paired-end and filter out any proper-pair flagged reads not in F/R orientation. -F --filtered-flag [int] Flag value of reads to exclude in allele counting default: [3852].
- -v --version
-
Display version number.
- -h --help
-
Display this usage information.
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.