Randomly pick variants from VCF file for 10000 iteration

Question

[tasnimul35-241]

Hi ,

I have a multisample VCF file containing nearly 6k variants. I want to pick randomly 1 variant at each iteration from total 10000 iteration and check whether this variant is present in another two vcf file. If its present in first vcf file and not in the second one, how I can count them?

[iraun]

Hi! What is the question exactly? How to pick a random variant in a VCF? How to make an iteration? How to find a variant in a VCF? How to count the matches?

[tasnimul35-241]

Yes. Kind of all of them

[Jeremy Leipzig]

What exactly does it mean for the VCF to have a variant? That one or more samples have the variant? Why not just combine these VCF files and count samples that are not 0/0 or ./.?

[tasnimul35-241]

It would be a great help if you please share a pseudocode for this.

Answer 1

[Pierre Lindenbaum]

1) extract the intervals with bcftools query 2) run a loop on the intervals file , pipe in shuf 3) for each random interval , search the variant with bcftools view

[tasnimul35-241]

As I am a newbee in Bioinformatics. Can you please suggest a code?

[tasnimul35-241]

It would be a great help if you please share a pseudocode for this.