jsa.hts.errorAnalysis assesses the error profile of sequencing data by getting the numbers of errors (mismatches, indels etc) from a bam file. Obviously, it does not distinguish sequencing errors from mutations, and hence consider mutations as errors. It is best to use with the bam file from aligning sequencing reads to a reliable assembly of the sample.
jsa.hts.errorAnalysis: Error analysis of sequencing data
jsa.hts.errorAnalysis [options]
- --bamFile=s Name of bam file
(REQUIRED)
- --reference=s Name of reference genome
(REQUIRED)
- --pattern=s Pattern of read name, used for filtering
(default='null')
- --qual=i Minimum quality required
(default='0')
- --help Display this usage and exit
(default='false')