Repo to hold vcf_processing_scripts
Install dependancies:
brew install samtools
brew install tabix
pip install pysam
Clone repo and update submodule:
$ git clone https://github.com/ngcrawford/vcf_conversion_scripts.git
$ cd vcf_conversion_scripts/
$ git submodule update --init
Bgzip and index vcf file:
bgizp my.vcf
tabix -p vcf my.vcf.gz
Create the .lik and .snps files:
cd vcf_conversion_scripts/
./vcf2DBMAdmix.py \
-i path/2/my.vcf.gz \
-l path/2/my.lik \
-s path/2/my.snps
Run DBM haplotype caller:
./dbm my -like