modules/gatk4_haplotypecaller

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

gatk4haplotypehaplotypecaller

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/haplotypecaller

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:false ]

`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:false ]

`*.vcf.gz`
`:file`

Compressed VCF file

*.vcf.gz

`tbi`

`meta`
`:map`

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

`*.tbi`
`:file`

Index of VCF file

*.vcf.gz.tbi

`bam`

`meta`
`:map`

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

`*.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.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590

modules/gatk4_haplotypecaller

Description

Input

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`intervals`
`:file`

`dragstr_model`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`dbsnp`
`:file`

`meta6`
`:map`

`dbsnp_tbi`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`bam`

`meta`
`:map`

`*.realigned.bam`
`:file`

`versions`

`versions.yml`
`:file`

Tools

gatk4
Apache-2.0

included in

maintainers

get in touch

modules/gatk4_haplotypecaller

Description

Input

meta:map

input:file

input_index:file

intervals:file

dragstr_model:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

meta5:map

dbsnp:file

meta6:map

dbsnp_tbi:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.tbi:file

bam

meta:map

*.realigned.bam:file

versions

versions.yml:file

Tools

gatk4 Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`intervals`
`:file`

`dragstr_model`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`meta5`
`:map`

`dbsnp`
`:file`

`meta6`
`:map`

`dbsnp_tbi`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`bam`

`meta`
`:map`

`*.realigned.bam`
`:file`

`versions`

`versions.yml`
`:file`

gatk4
Apache-2.0