Count the number of ROD objects encountered along the reference
java -jar GenomeAnalysisTK.jar -T CountRODsByRef -R reference.fasta -o output.txt --rod input.vcf
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Inputs | |||
| --rod | [] | Input VCF file(s) | |
| Optional Flags | |||
| --showSkipped  -s | false | If true, this tool will print out the skipped locations | |
| --verbose  -v | false | If true, this tool will print out detailed information about the rods it finds and locations | |