Description

endorS.py calculates endogenous DNA from samtools flagstat files and print to screen

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

stats_raw (file)

output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed

stats_qualityfiltered (file)

output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d

stats_deduplicated (file)

output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

json (file)

file with the endogenous DNA calculation tailored for multiQC

*_mqc.json
author
Github user aidaanva
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Tools

endorspy
GPL v3

endorS.py calculates percent on target and/or clonality from samtools flagstat files and print to screen

github.com/aidaanva/endorS.py 10.7717/peerj.10947