Calculate read counts per allele for allele-specific expression analysis
java -jar GenomeAnalysisTK.jar -R reference.fasta -T ASEReadCounter -o file_name.csv -I input.bam -sites sites.vcf -U ALLOW_N_CIGAR_READS [-minDepth 10] [--minMappingQuality 10] [--minBaseQuality 2] [-drf DuplicateRead]
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--sitesVCFFile  -sites | NA | Undocumented option | |
Optional Outputs | |||
--out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
Optional Parameters | |||
--countOverlapReadsType  -overlap | COUNT_FRAGMENTS_REQUIRE_SAME_BASE | Handling of overlapping reads from the same fragment | |
--minBaseQuality  -mbq | 0 | Minimum base quality | |
--minDepthOfNonFilteredBase  -minDepth | -1 | Minimum number of bases that pass filters | |
--minMappingQuality  -mmq | 0 | Minimum read mapping quality | |
--outputFormat | RTABLE | Format of the output file, can be CSV, TABLE, RTABLE |