Description

A Python application to generate self-contained HTML reports for variant review and other genomic applications

Input

name:type
description
pattern

meta{:bash}

:map

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

sites{:bash}

:file

VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites

tracks{:bash}

:file

List of any set of files of the types that IGV can display, eg BAM/CRAM, GTF/GFF, VCF, BED, etc

tracks_indices{:bash}

:file

List of indices for the tracks

meta2{:bash}

:map

Groovy Map containing genome information e.g. [ id:‘genome_name’ ]

fasta{:bash}

:file

Reference fasta file

*.{fasta,fa}

fai{:bash}

:file

Reference fasta file index

*.{fai}

Output

name:type
description
pattern

report{:bash}

meta{:bash}

:file

html report with a table of genomic sites and an embedded IGV genome browser for viewing data for each site

*.{html}

*.html{:bash}

:file

html report with a table of genomic sites and an embedded IGV genome browser for viewing data for each site

*.{html}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

igvreports
MIT

Creates self-contained html pages for visual variant review with IGV (igv.js).

github.com/igvteam/igv-reports 10.1093/bioinformatics/btac830
maintainer
Github user souljamie
get in touch
Ask a question on Slack Open an issue on GitHub