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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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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

In order to run build_fingerprint_maps, you must have working installations of:

  1. Python (>=2.7)
  2. PLINK2 -
  3. VCFTools -
  4. Anaconda( or the following modules: a. subprocess b. os c. itertools d. numpy e. sys f. argparse g. traceback h. time i. datetime
  5. LDSC -

Required Files

  1. 1000 Genomes Phase 3 VCFs(hg19) -
  2. 1000 Genomes Phase 3 Recombination maps(hg19) -

How to run

See to see a sample run script. Run python -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 for issues.


Nauman Javed(Broad Institute)

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