Description

Filters the raw output of sentieon/tnhaplotyper2.

Input

Name (Type)
Description
Pattern

meta (map)

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

meta2 (map)

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

meta3 (map)

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

vcf (file)

compressed vcf file from tnhaplotyper2

*.vcf.gz

vcf_tbi (file)

Tabix index of vcf file

*vcf.gz.tbi

stats (file)

Stats file that pairs with output vcf file

*vcf.gz.stats

contamination (file)

the location and file name of the file containing the contamination information produced by ContaminationModel.

*.contamination_data.tsv

segments (file)

the location and file name of the file containing the tumor segments information produced by ContaminationModel.

*.segments

orientation_priors (file)

the location and file name of the file containing the orientation bias information produced by OrientationBias.

*.orientation_data.tsv

fasta (file)

The reference fasta file

*.fasta

fai (file)

Index of reference fasta file

*.fasta.fai

Output

Name (Type)
Description
Pattern

vcf (file)

file containing filtered tnhaplotyper2 calls.

*.vcf.gz

vcf_tbi (file)

tbi file that pairs with vcf.

*.vcf.gz.tbi

stats (file)

file containing statistics of the tnfilter run.

*.stats

versions (file)

File containing software versions

versions.yml
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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