Description

Filtering, downsampling and profiling alignments in BAM/CRAM formats

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/CRAM file

*.{bam,cram}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bam (file)

Filtered or downsampled BAM file

*.{bam}
author
Github user bjohnnyd
get in touch
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Tools

variantbam
Apache-2.0

Filtering and profiling of next-generational sequencing data using region-specific rules

github.com/walaj/VariantBam github.com/walaj/VariantBam#table-of-contents https://github.com/walaj/VariantBam 10.1093/bioinformatics/btw111