panTro6 maf to vcf conversion

This repo contains the code to convert hg19.panTro6.synNet.maf.gz to an all sites vcf file where the only individual is panTro6 and is homozygous at every site. It should be noted that the code in this repo was inspired by Simon Martin's genomics_general repo that I repurposed for my own specific use. In this README.md I will outline the steps for the maf to vcf conversion.

Step 1: Download hg19.panTro6.synNet.maf.gz

This can be done a lot of different ways, but here is how I did it.

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro6/hg19.panTro6.synNet.maf.gz

Step 2: Run chimp_maf_parser.py

Once hg19.panTro6.synNet.maf.gz has been downloaded the next step is to extract the allele calls for panTro6, which can be accomplished with the following code.

for CHR in {1..22} X; do
module load tabix python/3.7.4; python3 chimp_maf_parser.py hg19.panTro6.synNet.maf.gz ${CHR} | bgzip > hg19_panTro6_chr${CHR}.txt.gz
done

Step 3: Run chimp_maf_output_to_vcf.py

Now that all of the genotype information has been extracted for panTro6 the next step is to convert that information into a vcf file, which can be accomplished with the following code and the generic_vcf_header.txt.

for CHR in {1..22} X; do
module load tabix python/3.7.4; python3 chimp_maf_output_to_vcf.py hg19_panTro6_chr${CHR}.txt.gz | bgzip > hg19_panTro6_chr${CHR}.vcf.gz
done

Step 4: Index the vcf files

Now that all panTro6 data has been converted to a vcf the last step is to create index files for those vcf files, which can be accomplished with the following code.

for VCF in *.vcf.gz; do
module load tabix; tabix -p vcf ${VCF}
done