Description

Call germline SNPs and indels via local re-assembly of haplotypes

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM file from alignment

*.{bam,cram}

input_index (file)

BAI/CRAI file from alignment

*.{bai,crai}

intervals (file)

Bed file with the genomic regions included in the library (optional)

dragstr_model (file)

Text file containing the DragSTR model of the used BAM/CRAM file (optional)

*.txt

meta2 (map)

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

fasta (file)

The reference fasta file

*.fasta

meta3 (map)

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

fai (file)

Index of reference fasta file

fasta.fai

meta4 (map)

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

dict (file)

GATK sequence dictionary

*.dict

meta5 (map)

Groovy Map containing dbsnp information
e.g. [ id:‘test_dbsnp’ ]

dbsnp (file)

VCF file containing known sites (optional)

meta6 (map)

Groovy Map containing dbsnp information
e.g. [ id:‘test_dbsnp’ ]

dbsnp_tbi (file)

VCF index of dbsnp (optional)

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

vcf (file)

Compressed VCF file

*.vcf.gz

tbi (file)

Index of VCF file

*.vcf.gz.tbi

bam (file)

Assembled haplotypes and locally realigned reads

*.realigned.bam
included in
rnavar sarek
maintainers
Github user suzannejin
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4
Apache-2.0

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/categories/360002369672s 10.1158/1538-7445.AM2017-3590