Download LD blocks

This is a short tutorial on how to download ld block data as summarized by Berisa and Pickrell. The LD data is available in hg19 genome build and for three different populations i.e. AFR, ASN and EUR.

First download the data from the bit bucket repository

git clone https://bitbucket.org/nygcresearch/ldetect-data.git

If you need the LD blocks for use with data in a different genome build then you will need to do a liftover.

To demonstrate how to lift over the ld block co-ordinates from hg19 to hg18 we will use the EUR LD blocks

1. Identify the data location

less ./EUR/fourier_ls-all.bed

2. Using a custom script do the lift over

python liftover_blocks.py -input ./EUR/fourier_ls-all.bed -output hg38_fourier_ls-all.bed.gz

Check out for error messages in your liftover process

The liftover_blocks.py is a custom script that contains this info;

#!/usr/bin/env python3

import gzip
import pyliftover

def _l(liftover, chr, pos):
    _new_chromosome = "NA"
    _new_position = "NA"
    try:
        pos = int(pos)
        l_ = liftover.convert_coordinate(chr, pos)
        if l_:
            if len(l_) > 1:
                print("Liftover with more than one candidate: %s", t.variant_id)
            _new_chromosome = l_[0][0]
            _new_position = int(l_[0][1])
    except:
        pass
    return _new_chromosome, _new_position

def run(args):
    print("starting lifting over.")
    liftover = pyliftover.LiftOver('hg19', 'hg38') # change genome builds here
    with gzip.open(args.output, "w") as _o:
        line = "{}\n".format("\t".join(["chr", "start", "stop"]))
        _o.write(line.encode())
        with open(args.input) as _i:
            for i,line in enumerate(_i):
                try:
                    comps = line.strip().split()
                    chrom = 'chr' + str(comps[0])
                    chrom = str(comps[0])
                    start = int(comps[1])
                    end = int(comps[2])

                    _chrs, _s = _l(liftover, chrom, start)
                    _chre, _e = _l(liftover, chrom, end)
                    if _chrs != _chre:
                        print("{}:{}:{} have different target chromosomes: {}/{}".format(chr, start, end, _chrs, _chre))
                    line = "{}\n".format("\t".join([_chrs, str(_s), str(_e)]))
                    _o.write(line.encode())
                except Exception as e:
                    print("Error for: %s", line)

    print("Finished lifting over.")

if __name__ == "__main__":
    import argparse
    parser = argparse.ArgumentParser("Liftover ld regions file")
    parser.add_argument("-input", help="region file")
    parser.add_argument("-output", help="Where the output should go")
    args = parser.parse_args()

    run(args)