bcftools isec outputs all variants instead of just the common variants

[celinehohzm]

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.vcf still 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 not all are in common?

Thanks!

[pd3]

I doubt this is a bug in bcftools. Is it possible that the numbers reflect different number of header lines, rather than different number of data lines? Try bcftools view -H isec_ABCD_ref/0000.vcf | wc -l.