Filtering vcf file for variants - including non-selected variants

Question

[andrebolerbarros]

Hey everyone,

I have a list of variants of interest. I am using a .tsv file to filter both cohorts (reference cohort + patient cohort) using bcftools.

My main problem is, even when using a .tsv file, I know bcftools transforms it into an interval (CHROM POS-1 POS). Therefore, my final vcf contains both POS-1 and POS, while I just wanted POS.

bcftools view -R ListVariants.txt control.vcf.gz -O z > 02_finalVCF/control_final.vcf.gz
bcftools view -R ListVariants.txt patient.vcf.gz -O z > 02_finalVCF/patient_final.vcf.gz

I have also used a .bed file but, as I expect, the problem remains the same.

Is there any way to get only the positions for the variants and not additional positions?

Thanks in advance!

[Pierre Lindenbaum]

may be you want bcftools isec

[andrebolerbarros]

Hey Pierre Lindenbaum! Thanks for your answer.

Unfortunately, this does not seem to work as well...

I had to use the variant list with -T criteria but, still have ~ 180 additional variants that I am supposed to.