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

vcf

meta:map

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

]

*.vcf.gz:file

Compressed VCF file

*.vcf.gz

tbi

meta:map

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

]

*.tbi:file

Index of VCF file

*.vcf.gz.tbi

bam

meta:map

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

]

*.realigned.bam:file

Assembled haplotypes and locally realigned reads

*.realigned.bam

versions

versions.yml:file

File containing software versions

versions.yml

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.