build_fingerprint_maps is a tool for building haplotype maps for use with Picardtools fingerprinting software. A haplotype map is a collection of "blocks" of SNPs which are in tight linkage with SNPs of the same block and low linkage with SNPs of different blocks.
In order to download
build_fingerprint_maps, you should clone this repository via the command
git clone https://github.com/naumanjaved/fingerprint_maps.git
In order to run
build_fingerprint_maps, you must have working installations of:
- Python (>=2.7)
- PLINK2 - https://www.cog-genomics.org/plink2
- VCFTools - http://vcftools.sourceforge.net/man_latest.html
- Anaconda(https://anaconda.org/anaconda/python) or the following modules:
- LDSC - https://github.com/bulik/ldsc
- 1000 Genomes Phase 3 VCFs(hg19) - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
- 1000 Genomes Phase 3 Recombination maps(hg19) - http://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3/
How to run
See run.sh to see a sample run script. Run python build_fingerprint_maps.py -h to see a list of command line options.
Use with Picardtools
Before using with Picardtools, append the file called "header" to the beginning of a map file.
Email email@example.com for issues.
Nauman Javed(Broad Institute)