Description

NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR).

Input

name:type
description
pattern

meta:map

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

bam:file

BAM file

*.bam

meta2:map

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

bam_index:file

BAM index file

*.bai

meta3:map

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

bqsr_table:file

Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator.

*.table

meta4:map

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

intervals:file

intervals

meta5:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

fasta:file

Reference fasta - must be unzipped.

*.fasta

Output

name:type
description
pattern

bam

meta:map

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

*.bam:file

BAM file after applying BQSR.

*.bam

bai

meta:map

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

*.bai:file

bai index corresponding to output bam file.

*.bai

versions

versions.yml:file

File containing software versions.

versions.yml

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/latest
Github user bsiranosian
Github user famosab
Ask a question on Slack Open an issue on GitHub