modules/stitch

STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format.

imputationgenomicsvcfbgencrambamsam

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

Description

Input

name:type

description

pattern

`meta:map`

Groovy Map containing information about the set of samples e.g. [ id:'test' ]

`collected_crams:file`

List of sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

`collected_crais:file`

List of BAM/CRAM/SAM index files

*.{bai,crai,sai}

`cramlist:file`

Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path.

*.txt

`samplename:file`

(Optional) File with list of samples names in the same order as in bamlist to impute. One file per line.

*.{txt}

`posfile:file`

Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the --posfile argument of STITCH for more information.

*.tsv

`input:directory`

Folder of pre-generated input RData objects used when STITCH is called with the --regenerateInput FALSE flag. It is generated by running STITCH with the --generateInputOnly TRUE flag.

input

`rdata:directory`

Folder of pre-generated input RData objects used when STITCH is called with the --regenerateInput FALSE flag. It is generated by running STITCH with the --generateInputOnly TRUE flag.

RData

`chromosome_name:string`

Name of the chromosome to impute. Should match a chromosome name in the reference genome.

`K:integer`

Number of ancestral haplotypes to use for imputation. Refer to the documentation for the --K argument of STITCH for more information.

`nGen:integer`

Number of generations since founding of the population to use for imputation. Refer to the documentation for the --nGen argument of STITCH for more information.

`meta2:map`

Groovy Map containing information about the reference genome used e.g. [ id:'test' ]

`fasta:file`

FASTA reference genome file

*.{fa,fasta}

`fasta_fai:file`

FASTA index file

*.{fai}

`seed:integer`

Seed for random number generation

Output

name:type

description

pattern