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Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.
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README.md

build_fingerprint_maps

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.

Dependencies

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:

  1. Python (>=2.7)
  2. PLINK2 - https://www.cog-genomics.org/plink2
  3. VCFTools - http://vcftools.sourceforge.net/man_latest.html
  4. Anaconda(https://anaconda.org/anaconda/python) or the following modules: a. subprocess b. os c. itertools d. numpy e. sys f. argparse g. traceback h. time i. datetime
  5. LDSC - https://github.com/bulik/ldsc

Required Files

  1. 1000 Genomes Phase 3 VCFs(hg19) - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
  2. 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.

Support

Email javed@broadinstitute.org for issues.

Authors

Nauman Javed(Broad Institute)

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