Description

Manipulation, validation and exploration of pedigrees

Input

name:type
description
pattern

meta{:bash}

:map

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

vcf{:bash}

:file

VCF file

*.vcf.gz

vcf_tbi{:bash}

:file

TBI file

*.vcf.gz.tbi

meta2{:bash}

:map

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

ped{:bash}

:file

PED/FAM file

*.{ped,fam}

meta3{:bash}

:map

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

sites{:bash}

: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{:bash}

meta{:bash}

:map

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

${prefix}.vs.html{:bash}

:file

HTML file comparison between reported and inferred sex

*.vs.html

html{:bash}

meta{:bash}

:map

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

${prefix}.html{:bash}

:file

HTML report

*.html

ped{:bash}

meta{:bash}

:map

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

*.peddy.ped{:bash}

:file

Inferred PED file

*.peddy.ped

het_check_png{:bash}

meta{:bash}

:map

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

*.het_check.png{:bash}

: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{:bash}

meta{:bash}

:map

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

*.ped_check.png{:bash}

:file

PNG file containing pedigree check between reported and inferred sex

*.het_check.png

sex_check_png{:bash}

meta{:bash}

:map

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

*.sex_check.png{:bash}

: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{:bash}

meta{:bash}

:map

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

*.het_check.csv{:bash}

: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{:bash}

meta{:bash}

:map

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

*.ped_check.csv{:bash}

:file

CSV file containing pedigree check between reported and inferred sex

*.het_check.csv

sex_check_csv{:bash}

meta{:bash}

:map

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

*.sex_check.csv{:bash}

: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{:bash}

meta{:bash}

:map

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

*.ped_check.rel-difference.csv{:bash}

:file

CSV file with the comparison between inferred and given relatedness

*.ped_check.rel-difference.csv

versions{:bash}

versions.yml{:bash}

: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
included in
raredisease
maintainer
Github user rannick
get in touch
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