alleleCounter1
Ngs copy number algorithms
Usage
alleleCounter -l
loci_file.txt
-b
sample.bam
-o
output.txt
[-m
int]
[-r
ref.fa.fai]
Overview
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
-band 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.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).