Description

Perform basic quality control on a BAM file generated with Biscuit

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file produced using Biscuit

Output

Name (Type)
Description
Pattern

biscuit_qc_reports (file)

Summary files containing the following information:

  • CpG retention by position in read
  • CpH retention by position in read
  • Read duplication statistics
  • Insert size distribution
  • Distribution of mapping qualities
  • Proportion of reads mapping to each strand
  • Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT
*.txt

versions (file)

File containing software versions

versions.yml
author
Github user njspix
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Tools

biscuit
MIT

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-qc https://github.com/huishenlab/biscuit