Resources

A C++ program for inferring biological relatedness between pairs of individuals from 2nd generation sequencing data using maximum-likelihood that is particularly effective when read coverage is low. The program is written in collaboration with Rob Patro

A python program that calls genotypes from bam files at positions/regions specified in a bam file while taking into account post mortem damage as estimate by MapDamage

ATLAS (Analysis Tools for Low-coverage and Ancient Samples) is a package that covers all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute. ATLAS is developed by Dan Wegmann

A python script for estimating allele frequencies from Pool-Seq data using the method of Lynch et al. GBE.2014

A python script takes a vcf file and calculates allele frequencies using genotype likelihoods for a subset of individuals at specific loci using the method of Kim et al. 2011 BMC Bioinformatics