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

*.bam.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.

*.bam.bai

versions_parabricks

${task.process}

:string

The process the versions were collected from

parabricks

:string

The tool name

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

parabricks

:string

The tool name

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'

:string

The command used to generate the version of the tool

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/latest
maintainers
Github user bsiranosian
Github user famosab
get in touch
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