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 | |