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bgen

fast bgen parser for python

cifer

CNV inheritance from exome read-depth

clinical-filter

filtering trio-based genetic variants in VCFs for clinical review

count_singletons

code to identify conserved sites at the last base of exons, and count singletons

ddd_4k

denovofilter

Rules for filtering candidate de novo sites

denovonear

analysing proximity clustering of de novo variants in genes

dnm_cohorts

package for published de novo datasets in rare disease

fitdnm

Enrichment of de novo mutations within genes

gencodegenes

loads genes from GENCODE GTF files

hpo_similarity

Analysis of similarity of HPO terms in groups of individuals

ld_estimator

calculate linkage disequilibrium between pairs of variants

liftover

liftover for python, made fast with cython

mosaic_de_novos

code to call mosaic de novo SNVs

mupit

De novo mutation recurrence significance testing

mutation_weights

peds

basic pedigree file parsing

publisheddenovos

R data package for published de novo variants from exome and genome sequencing studies of children with developmental disorders

pybcf

readdepth

small package to calculate read depth in BAMs

recessivestats

repository for analysis of recessive genes

regressor

linear regression cython

scikit-hep

Metapackage of Scikit-HEP project data analysis packages for Particle Physics.

severity_sampler

test severity of de novo mutations

shabam

A python tool to create sequence plots from bam/cram files.

snphwe

python implementation of SNPHWE fast exact hardy-weinberg

vcfremapper

convert VCFs between different genome builds

vcfsyncer

use multiple single-sample VCFs as if they were from one multi-sample VCF