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# 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
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