Description

command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.

Input

Name (Type)
Description
Pattern

meta (map)

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

input_file (file)

BAM/CRAM/SAM file

*.{bam,cram}

index (file)

bam file index

*.{bai,crai}

fasta (file)

specifies reference genome file (only for cram file without reference genome)

*.{fasta,fasta.gz,fa,fa.gz}

fai (file)

Index of reference fasta file

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

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

pytor (file)

read depth root file in which read depth data binned to 100 base pair bins will be stored.

*.{pytor}

versions (file)

File containing software versions

versions.yml
maintainers
Github user sima-r
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

cnvpytor -rd
MIT

calling CNVs using read depth

github.com/abyzovlab/CNVpytor 10.1101/2021.01.27.428472v1