This tool will count the alleles in multiple bam files. It's posible to count alleles for each separated readgroup. This can be used for quality checks.
CountAlleles requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.
Download the latest version of CountAlleles here. To generate the usage run:
java -jar <CountAlleles_jar> --help
This tool require that in the bam files the readgroups are setup correctly to detect the sample and readgroup names. The input and output vcf file can be compressed, this is auto detected by the file extension.
Readgroup calling is optional and can be enabled with
Default run with 1 bam file:
java -jar <CountAlleles_jar> \ -R <reference_fasta> \ -I <input_vcf> \ -o <output_vcf> \ -b <input_bam>
Run with readgroups:
java -jar <CountAlleles_jar> \ -R <reference_fasta> \ -I <input_vcf> \ -o <output_vcf> \ -b <input_bam> \ --outputReadgroups
Usage for CountAlleles:
|Option||Required||Can occur multiple times||Description|
|--log_level, -l||no||no||Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'|
|--help, -h||no||no||Print usage|
|--version, -v||no||no||Print version|
|--inputFile, -I||yes||no||input VCF filename|
|--outputFile, -o||yes||no||output VCF filename|
|--bam, -b||no||yes (unlimited)||bam file, from which the variants (VCF files) were called|
|--bamList||no||yes (unlimited)||bam file, from which the variants (VCF files) were called|
|--min_mapping_quality, -m||no||no||minimum mapping quality score for a read to be taken into account|
|--referenceFasta, -R||yes||no||reference fasta|
|--outputReadgroups||no||no||Output each readgroup separated|
CountAlleles is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.
CountAlleles is build using sbt. Before submitting a pull request, make sure all tests can be passed by
sbt test from the project's root. We recommend using an IDE to work on CountAlleles. We have had
good results with this IDE.