modules/peddy

Manipulation, validation and exploration of pedigrees

pedigreespedfamily

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

Description

Manipulation, validation and exploration of pedigrees

Input

name:type

description

pattern

`meta:map`

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

`vcf:file`

VCF file

*.vcf.gz

`vcf_tbi:file`

TBI file

*.vcf.gz.tbi

`meta2:map`

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

`ped:file`

PED/FAM file

*.{ped,fam}

`meta3:map`

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

`sites:file`

sites file. By defaults peddy uses hg19/GRCh37, “—sites hg38” can be specified in the process argument or a custom file following syntax https://github.com/brentp/peddy/blob/master/peddy/GRCH37.sites can be provided

*.sites

Output

name:type

description

pattern

`vs_html`

`meta:map`

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

`${prefix}.vs.html:file`

HTML file comparison between reported and inferred sex

*.vs.html

`html`

`meta:map`

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

`${prefix}.html:file`

HTML report

*.html

`ped`

`meta:map`

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

`*.peddy.ped:file`

Inferred PED file

*.peddy.ped

`het_check_png`

`meta:map`

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

`*.het_check.png:file`

PNG file containing heterozygosity check. Rate of het calls, allele-balance at het calls, mean and median depth, and a PCA projection onto thousand genomes.

*.het_check.png

`ped_check_png`

`meta:map`

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

`*.ped_check.png:file`

PNG file containing pedigree check between reported and inferred sex

*.het_check.png

`sex_check_png`

`meta:map`

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

`*.sex_check.png:file`

PNG file with sex check performs a comparison between the sex reported in the ped file and that inferred from the genotypes on the non-PAR regions of the X chromosome.

*.sex_check.png

`het_check_csv`

`meta:map`

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

`*.het_check.csv:file`

CSV file containing heterozygosity check. Rate of het calls, allele-balance at het calls, mean and median depth, and a PCA projection onto thousand genomes.

*.het_check.csv

`ped_check_csv`

`meta:map`

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

`*.ped_check.csv:file`

CSV file containing pedigree check between reported and inferred sex

*.het_check.csv

`sex_check_csv`

`meta:map`

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

`*.sex_check.csv:file`

CSV file with sex check performs a comparison between the sex reported in the ped file and that inferred from the genotypes on the non-PAR regions of the X chromosome.

*.sex_check.csv

`ped_check_rel_difference_csv`

`meta:map`

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

`*.ped_check.rel-difference.csv:file`

CSV file with the comparison between inferred and given relatedness

*.ped_check.rel-difference.csv

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

peddy
MIT

genotype, ped correspondence check, ancestry check, sex check. directly, quickly on VCF

github.com/brentp/peddy peddy.readthedocs.io/en/latest https://github.com/brentp/peddy 10.1016/j.ajhg.2017.01.017

modules/peddy

Description

Input

meta:map

vcf:file

vcf_tbi:file

meta2:map

ped:file

meta3:map

sites:file

Output

vs_html

meta:map

${prefix}.vs.html:file

html

meta:map

${prefix}.html:file

ped

meta:map

*.peddy.ped:file

het_check_png

meta:map

*.het_check.png:file

ped_check_png

meta:map

*.ped_check.png:file

sex_check_png

meta:map

*.sex_check.png:file

het_check_csv

meta:map

*.het_check.csv:file

ped_check_csv

meta:map

*.ped_check.csv:file

sex_check_csv

meta:map

*.sex_check.csv:file

ped_check_rel_difference_csv

meta:map

*.ped_check.rel-difference.csv:file

versions

versions.yml:file

Tools

peddy MIT

`meta:map`

`vcf:file`

`vcf_tbi:file`

`meta2:map`

`ped:file`

`meta3:map`

`sites:file`

`vs_html`

`meta:map`

`${prefix}.vs.html:file`

`html`

`meta:map`

`${prefix}.html:file`

`ped`

`meta:map`

`*.peddy.ped:file`

`het_check_png`

`meta:map`

`*.het_check.png:file`

`ped_check_png`

`meta:map`

`*.ped_check.png:file`

`sex_check_png`

`meta:map`

`*.sex_check.png:file`

`het_check_csv`

`meta:map`

`*.het_check.csv:file`

`ped_check_csv`

`meta:map`

`*.ped_check.csv:file`

`sex_check_csv`

`meta:map`

`*.sex_check.csv:file`

`ped_check_rel_difference_csv`

`meta:map`

`*.ped_check.rel-difference.csv:file`

`versions`

`versions.yml:file`

peddy
MIT