compare.sh

# This is a record of comparisons made in the cyvcf2 paper. These vcf filenames are now different and may not work to run the tests
chrom=22

if [[ ! -e ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ]]; then
    wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
fi
if [[ ! -e ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ]]; then
    wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi
fi

echo "#bcftools"
time bcftools filter -e "N_ALT != 1 || QUAL < 20 || maf[0]>0.05" ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | grep -cv ^#

echo "#cyvcf2"
time python filter-cyvcf2.py ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

echo "#pysam"
time python filter-pysam.py ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

echo "#pyvcf"
time python filter-pyvcf.py ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz