bcftools isec outputs all variants instead of just the common variants

Question

[fafad046]

Hi,

I have two vcf files, ALL.autosomes.phase3.vcf.gz and concat_ABCD_release_2.0.1_r1_filtered.vcf.gz.

ALL.autosomes.phase3.vcf.gz has 2504 subjects, while concat_ABCD_release_2.0.1_r1_filtered.vcf.gz has 10501 subjects.

After doing bcftools isec -c none -n=2 -p isec_ABCD_ref ALL.autosomes.phase3.vcf.gz concat_ABCD_release_2.0.1_r1_filtered.vcf.gz to get the vcf with common variants in both vcf files,

I realized that the output file isec_ABCD_ref/0000.vcf and /0001.vcftill has the same number of subjects as the original files, which are 2540 and 10501 respectively.

May I know why is bcftools isec not working and outputs all the variants even when they are not in common?

Thanks!

[Pierre Lindenbaum]

is it the same nomenclature for the chromosomes ? 'chr1' vs '1' ?

[fafad046]

thanks for the reply! yes, they are both in the same nomenclature '1'...