Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome
java -jar GenomeAnalysisTK.jar -T CallableLoci -R reference.fasta -I myreads.bam -summary table.txt -o callable_status.bed
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Outputs | |||
| --summary | NA | Name of file for output summary | |
| Optional Outputs | |||
| --out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --maxDepth | -1 | Maximum read depth before a locus is considered poorly mapped | |
| --maxFractionOfReadsWithLowMAPQ Â -frlmq | 0.1 | If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped | |
| --maxLowMAPQ Â -mlmq | 1 | Maximum value for MAPQ to be considered a problematic mapped read. | |
| --minBaseQuality  -mbq | 20 | Minimum quality of bases to count towards depth. | |
| --minMappingQuality  -mmq | 10 | Minimum mapping quality of reads to count towards depth. | |
| Advanced Parameters | |||
| --format | BED | Output format | |
| --minDepth | 4 | Minimum QC+ read depth before a locus is considered callable | |
| --minDepthForLowMAPQ Â -mdflmq | 10 | Minimum read depth before a locus is considered a potential candidate for poorly mapped | |