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 file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file. It also requires to contain “@RG” header lines to annotation different readGroups (sequencing runs and lanes). The SM tag in the “@RG” header should match with one of the genotyped sample.

*.bam

bai:file

BAM index file BAI

*.bai

refvcf:file

The input VCF file contains (1) external genotype information and/or (2) allele frequency information as AF entry or AC/AN entries in the INFO field.

*.{vcf,vcf.gz}

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 verifyBamID result.

*.log

selfsm

meta:map

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

*.selfSM:file

Per-sample statistics describing how well the sample matches to the annotated sample.

*.selfSM

depthsm

meta:map

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

*.depthSM:file

The depth distribution of the sequence reads per sample

*.depthSM

selfrg

meta:map

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

*.selfRG:file

Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without —ignoreRG option)

*.selfRG

depthrg

meta:map

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

*.depthRG:file

The depth distribution of the sequence reads per readGroup. (available only without —ignoreRG option)

*.depthRG

bestsm

meta:map

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

*.bestSM:file

Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with —best option)

*.bestSM

bestrg

meta:map

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

*.bestRG:file

Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with —best and without —ignoreRG option)

*.bestRG

versions

versions.yml:file

File containing software versions

versions.yml

Tools

verifybamid
GPL v3

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.

genome.sph.umich.edu/wiki/VerifyBamID http://genome.sph.umich.edu/wiki/VerifyBamID https://github.com/statgen/verifyBamID 10.1016/j.ajhg.2012.09.004
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