jeremymcrae

liftover

liftover for python, made fast with cython

hpo_similarity

Analysis of similarity of HPO terms in groups of individuals

clinical-filter

filtering trio-based genetic variants in VCFs for clinical review

bgen

fast bgen parser for python

denovonear

analysing proximity clustering of de novo variants in genes

denovoFilter

Rules for filtering candidate de novo sites

regressor

linear regression cython

ld_estimator

calculate linkage disequilibrium between pairs of variants

mupit

De novo mutation recurrence significance testing

dnm_cohorts

package for published de novo datasets in rare disease

recessiveStats

repository for analysis of recessive genes

gencodegenes

loads genes from GENCODE GTF files

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

vcfsyncer

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

cifer

CNV inheritance from exome read-depth

count_singletons

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

ddd_4k

fitDNM

Enrichment of de novo mutations within genes

mosaic_de_novos

code to call mosaic de novo SNVs

mutation_weights

readDepth

small package to calculate read depth in BAMs

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