OICR note

This fork contains map files with OICR compatible headers:

• oicr_hg19_chr.map
• oicr_hg38_chr.map

The map files were created with oicr_create_map_files.sh

Smaller map files, which allow for faster running of crosscheckFingerprints, are described in the comments of a Broad blog post and were downloaded from the Broad Google Cloud website:

• oicr_hg19_v0_Homo_sapiens_assembly19.with_assay_info.haplotype_database.txt
• oicr_hg38_v0_Homo_sapiens_assembly38.with_assay_info.haplotype_database.txt

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.

In order to download build_fingerprint_maps, you should clone this repository via the command

git clone https://github.com/naumanjaved/fingerprint_maps.git

Precomputed map files

• hg19 with "chr" prefix
• hg19 without "chr" prefix
• hg38 with "chr" prefix
• hg38 without "chr" prefix

The map_files directory also contains pre-computed maps with relaxed intra- and inter- block correlation thresholds. Map names contain the parameters used.

Dependencies

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(LDScore regression)

Required Files

Fingerprint maps uses VCFs from 1000 Genomes Phase 3 and recombination maps(SHAPEIT format). These can be found here:

• hg19 and hg38 liftover VCFs
• hg19 recombination maps from SHAPEIT
• hg38 recombination maps from SHAPEIT liftover

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 appropriate header file to the beginning of the map file:

• hg19 with "chr" prefix
• hg19 without "chr" prefix
• hg38 with "chr" prefix
• hg38 without "chr" prefix

Support

Email javed@broadinstitute.org for issues.

Authors

Nauman Javed(Broad Institute)