Dr Lachlan J Coin

 I am  working on various statistical and mathematical problems in genomics. I am particularly interested in building mathematical models to identify genetic variants in high-throughput genomics data - including genotyping microarrays and next generation sequence data - with the ultimate aim of understanding the functional impact and evolutionary history of these variants.

ECCB 2012 report:  ECCB meeting report

Software:  

Yhap  software for identifying haplogroups from low coverage sequence data: Yhap_0.51

ExomeCNVTest software : ExomeCNVTest_0.51

SOAP-popIndel  software for genotyping indels in exome data

SOAP-popIndel

cnvHiTSeq - software for detecting and genotyping CNVs in WGS data

cnvHitSeq

Toy example for cnvHitSeq

cnvPipe - software to enable CNV meta analysis

cnvPipe_v0.82

Software for converting  IMPUTE format to format used by MultiPhen software

convertImpute

MultiPhen software

MultiPhen

vntrTest

VNTRTest0.52

vntrTest is a program for assessing association of VNTR fragment length genotypes with either continuous or case-control outcomes. 

cnvHap

cnvHap is a program for joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.

cnvHapv1.033

polyHap

polyHap is a program for phasing polyploids and copy number regions. See http://dx.doi.org/10.1186/1471-2105-9-513 for more details.

The first version was designed just for phasing polyploid regions (with the restriction that the ploidy is fixed across the entire region of analysis).

polyHap(v1) (right click, and save-as polyHap.zip)

We have extended polyHap to remove this restriction, so that it can phase CNV regions (from pre-calculated CNV/SNP genotypes):

polyHapv2 (right click, and save-as polyHapv2.zip)

AncesHC

AncesHC is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome. See http://dx.doi.org/10.1093/bioinformatics/btn071 for more details.

AncesHC2009_1

metaMapper

metaMapper is a program for flexible, scalable GWAS meta-analysis and visualisation.

MetaMapper_1.01

invertFREGENE

Software for simulating sequence level data with inversions. See http://dx.doi.org/10.1093/bioinformatics/btq029 for more details. Developed in conjunction with Clive Hoggart and Paul O'Reilly.

• invertFREGENE.pdf
• invertFREGENE.tar.gz

Pseudogene inference from loss of constraint (PSILC)

Software for identifying pseudogenes via loss of evolutionary constraint: PSILC version 1.21

Supplementary data

Supplementary information  from paper "Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases"