alleleCounter - NGS copy number algorithms
alleleCounter -l loci_file.txt -b sample.bam -o
output.txt [-m int] [-r ref.fa.fai]
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).
- -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.
- -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.
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.