This repo doesn't contain data files; just the scripts we used to download and modify the data files.

wget "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit"
wget "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/md5sum.txt"

I then edited md5sum.txt to remove all lines except hg19.2bit and ran

md5sum -c md5sum.txt

The result confirms that hg19.2bit is okay.

I also downloaded twoBitToFa and faToTwoBit from

http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

and installed in my bin directory. bcftools needs the index, which requires a fasta file compressed with bgzip:

twoBitToFa hg19.2bit stdout | bgzip -c > hg19.fa.gz
samtools faidx hg19.fa.gz

Within hg19.2bit, the chromosomes are sorted in numerical order. Legofit files, on the other hand, sort chromosomes in lexical order. One could use numerically-sorted fasta files with legofit, because the fasta files are indexed, and bcftools could find the appropriate chromosome. But this would involve a lot of seeking back and forth within the file. It should speed things up to sort the fasta files in lexical order. The job below also removes "chr" from the name of each chromosome.

sbatch sort.slr

This creates hg19-sort.fa.gz, compressed with bgzip. Finally, index the sorted file:

samtools faidx hg19-sort.fa.gz