modules/verifybamid_verifybamid2

Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.

contaminationbamverifybamidDNA contamination estimation

https://github.com/nf-core/modules/[...]/modules/nf-core/verifybamid/verifybamid2

Description

Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`bai`
`:file`

BAI/CRAI/CSI index file

*.{bai,crai,csi}

`svd_ud`
`:file`

.UD matrix file from SVD result of genotype matrix

*.UD

`svd_mu`
`:file`

.mu matrix file of genotype matrix

*.mu

`svd_bed`
`:file`

.Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required]

*.bed

`refvcf`
`:file`

Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional]

*.vcf

`references`
`:file`

reference file [Required]

*.fasta

Output

name:type

description

pattern

`log`

`meta`
`:map`

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

`*.log`
`:file`

Detailed summary of the VerifyBamId2 results

*.log

`ud`

`meta`
`:map`

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

`*.UD`
`:file`

.UD matrix file from customized reference vcf input

*.UD

`bed`

`meta`
`:map`

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

`*.bed`
`:file`

.Bed file from customized reference marker vcf input

*.bed

`mu`

`meta`
`:map`

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

`*.mu`
`:file`

.mu matrix file of genotype matrix from customized reference vcf input

*.mu

`self_sm`

`meta`
`:map`

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

`*.selfSM`
`:file`

Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level.

*.selfSM

`ancestry`

`meta`
`:map`

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

`*.Ancestry`
`:file`

Ancestry information

*.Ancestry

`versions_verifybamid2`

`${task.process}`
`:string`

The name of the process

`verifybamid2`
`:string`

The name of the tool

`verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`verifybamid2`
`:string`

The name of the tool

`verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'`
`:eval`

The expression to obtain the version of the tool

Tools

verifybamid2
MIT

A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

http://griffan.github.io/VerifyBamID https://github.com/Griffan/VerifyBamID 10.1101/gr.246934.118

modules/verifybamid_verifybamid2

Description

Input

meta:map

bam:file

bai:file

svd_ud:file

svd_mu:file

svd_bed:file

refvcf:file

references:file

Output

log

meta:map

*.log:file

ud

meta:map

*.UD:file

bed

meta:map

*.bed:file

mu

meta:map

*.mu:file

self_sm

meta:map

*.selfSM:file

ancestry

meta:map

*.Ancestry:file

versions_verifybamid2

${task.process}:string

verifybamid2:string

verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p':eval

Topics

versions

${task.process}:string

verifybamid2:string

verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p':eval

Tools

verifybamid2 MIT

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`svd_ud`
`:file`

`svd_mu`
`:file`

`svd_bed`
`:file`

`refvcf`
`:file`

`references`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`ud`

`meta`
`:map`

`*.UD`
`:file`

`bed`

`meta`
`:map`

`*.bed`
`:file`

`mu`

`meta`
`:map`

`*.mu`
`:file`

`self_sm`

`meta`
`:map`

`*.selfSM`
`:file`

`ancestry`

`meta`
`:map`

`*.Ancestry`
`:file`

`versions_verifybamid2`

`${task.process}`
`:string`

`verifybamid2`
`:string`

`verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'`
`:eval`

`versions`

`${task.process}`
`:string`

`verifybamid2`
`:string`

`verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'`
`:eval`

verifybamid2
MIT