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{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai{:bash}

:file

BAI/CRAI/CSI index file

*.{bai,crai,csi}

svd_ud{:bash}

:file

.UD matrix file from SVD result of genotype matrix

*.UD

svd_mu{:bash}

:file

.mu matrix file of genotype matrix

*.mu

svd_bed{:bash}

:file

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

*.bed

refvcf{:bash}

:file

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

*.vcf

references{:bash}

:file

reference file [Required]

*.fasta

Output

name:type
description
pattern

log{:bash}

meta{:bash}

:map

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

*.log{:bash}

:file

Detailed summary of the VerifyBamId2 results

*.log

ud{:bash}

meta{:bash}

:map

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

*.UD{:bash}

:file

.UD matrix file from customized reference vcf input

*.UD

bed{:bash}

meta{:bash}

:map

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

*.bed{:bash}

:file

.Bed file from customized reference marker vcf input

*.bed

mu{:bash}

meta{:bash}

:map

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

*.mu{:bash}

:file

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

*.mu

self_sm{:bash}

meta{:bash}

:map

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

*.selfSM{:bash}

:file

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

*.selfSM

ancestry{:bash}

meta{:bash}

:map

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

*.Ancestry{:bash}

:file

Ancestry information

*.Ancestry

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
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