IBDMUT

Reference: P.F. Palamara, L. Francioli, P. Wilton, G. Genovese, A. Gusev, H. Finucane, S. Sankararaman, GoNL Consortium, S. Sunyaev, P. de Bakker, J. Wakeley, I. Pe’er, A. Price, "Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates", American Journal of Human Genetics, 2015.

Contact: Pier Palamara, ppalama AT hsph DOT harvard DOTAGAIN edu

IBDMUT Infers mutation and gene conversion rates using identical-by-descent segments

Usage

Options:

--demography [file] (demographic model with format "generation	size" for each line. Sizes are haploid)
--plink [fileRoot] (plink file root; expects .ped.gz, .map, and .frq)
--match [file] (match.gz file in GERMLINE format)

Some of the optional or alternative flags:

--MaAFRegression [intValueFromCount] [intValueStep] [intValueToCount] (from MAF counts, interval MAF counts, to MAF counts)
--offsetCM [value] (distance to be excluded from edges; default: 0.0)
--lenRange [fromLen] [toLen] (default: 2.0 5.0)
--plinkList [file] (substitutes --plink and --match for many files)
--jackknife (only if --plinkList is used with several independent regions)
--saveBin [suffix] (saves a binary file, which will load much faster than the ped.gz file)
--loadBin [suffix] (load a binary file)
--mask [file] (bed file with regions to be included in analysis)
--maskList [file] (substitutes --mask for many files)
--threads [value] (default: 1)

Example

java -jar IBDMUT.jar \
	--plinkList EXAMPLES/plinkList.txt \
	--demography EXAMPLES/10K.demo \
	--lenRange 1.6 5.0 \
	--offsetCM 0.5 \
	--MaAFRegression 50 5 250 \
	--saveBin .save \
	--jackknife \
	--threads 4

Dependencies

(all in lib folder)

Kryo: https://github.com/EsotericSoftware/kryo

Minlog: https://github.com/EsotericSoftware/minlog/

Objenesis: https://github.com/easymock/objenesis

Reflactasm: https://github.com/EsotericSoftware/reflectasm