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{:bash}

:map

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

input_file{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram}

index{:bash}

:file

bam file index

*.{bai,crai}

fasta{:bash}

:file

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

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

fai{:bash}

:file

Index of reference fasta file

*.fai

Output

name:type
description
pattern

pytor{:bash}

meta{:bash}

:map

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

*.pytor{:bash}

:file

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

*.{pytor}

versions{:bash}

versions.yml{:bash}

: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
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