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’ ]

input (file)

bam file for sample to be variant called.

*.bam

input_index (file)

bai index corresponding to input bam file. Only necessary if intervals are provided.

*.bai

bqsr_table (file)

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

*.table

interval_file (file)

File or files containing genomic intervals for use in base quality score recalibration.

*.{bed,interval_list,picard,list,intervals}

fasta (file)

Reference fasta - must be unzipped.

*.fasta

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions.

versions.yml

bam (file)

BAM file after applying BQSR.

*.bam

bai (file)

bai index corresponding to output bam file.

*.bai
author
Github user bsiranosian
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Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks