Description

Collects multiple quality metrics from a bam file

Input

Name (Type)
Description
Pattern

meta (map)

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

meta2 (map)

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

meta3 (map)

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

bam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

bai (file)

Index of th sorted BAM/CRAM/SAM file

*.{bai,crai,sai}

fasta (file)

Genome fasta file

*.{fa,fasta}

fai (file)

Index of the genome fasta file

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

mq_metrics (file)

File containing the information about mean base quality score for each sequencing cycle

*.txt

qd_metrics (file)

File containing the information about number of bases with a specific base quality score

*.txt

gc_summary (file)

File containing the information about GC bias in the reference and the sample

*.txt

gc_metrics (file)

File containing the information about GC bias in the reference and the sample

*.txt

aln_metrics (file)

File containing the statistics about the alignment of the reads

*.txt

is_metrics (file)

File containing the information about statistical distribution of insert sizes

*.txt
author
Github user ramprasadn
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Tools

sentieon

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon.com