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

pytor

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

versions.yml:file

File containing software versions

versions.yml

Tools

cnvpytor -rd
MIT

calling CNVs using read depth

github.com/abyzovlab/CNVpytor 10.1101/2021.01.27.428472v1
maintainers
Github user sima-r
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub