BGI-flexlab / bamqc

BGI-lowpass bam quality control

bamqc

BGI-lowpass bam quality control

Usage

usage: java -jar bamqc.jar [-c] [-h] -i <FILE> [-o <String>] -s <FILE>

Options:
 -c,--countSecondaryReads   The secondary alignment reads are counted and ignored by default [false]
 -h,--help                  Print this help.
 -i,--input <FILE>          input bam(BAM). [request]
 -o,--output <String>       report file [request]
 -s,--site <FILE>           reference panel site.vcfs list [request]