Description

estimates the parameters for the DRAGstr model

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

bam_index (file)

index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

intervals (file)

BED file or interval list containing regions (optional)

*.{bed,interval_list}

fasta (file)

The reference FASTA file

*.{fasta,fa}

fasta_fai (file)

The index of the reference FASTA file

*.fai

dict (file)

The sequence dictionary of the reference FASTA file

*.dict

strtablefile (file)

The StrTableFile zip folder of the reference FASTA file

*.zip

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

dragstr_model (file)

The DragSTR model

*.txt
maintainer
Github user nvnieuwk
get in touch
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Tools

gatk4
Apache-2.0

Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA- https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590