Samtools
Supported Tool
Samtools is a suite of programs for interacting with high-throughput sequencing data.
Description
The Samtools module parses results generated by Samtools, a suite of programs for interacting with high-throughput sequencing data.
Supported commands:
stats
flagstats
idxstats
rmdup
coverage
markdup
idxstats
The samtools idxstats
prints its results to standard
out (no consistent file name) and has no header lines
(no way to recognise from content of file). As such, idxstats
result files must have the string idxstat
somewhere in the filename.
There are a few MultiQC config options that you can add to customise how the idxstats module works. A typical configuration could look as follows:
File search patterns
samtools/stats:
contents: This file was produced by samtools stats
samtools/flagstat:
contents: in total (QC-passed reads + QC-failed reads)
samtools/idxstats:
fn: "*idxstat*"
samtools/rmdup:
contents: "[bam_rmdup"
samtools/coverage:
contents: "#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tm\
eanbaseq\tmeanmapq"
num_lines: 10
samtools/markdup_txt:
contents: "COMMAND: samtools markdup"
num_lines: 2
samtools/markdup_json:
contents: '"COMMAND": "samtools markdup'
num_lines: 10