Question: how to use bcftools isec to union two vcf files?
2
gravatar for blueskypie
5.7 years ago by
blueskypie50
United States
blueskypie50 wrote:

I have the following files:

A.vcf which contains one sample s1

B.vcf which contains one sample s1

region.bed

I'd like to merge A.vcf and B.vcf for sites in region.bed, and use A.vcf for sites present in both files. Here is my command but it does not work as I expected:

bcftools isec A.vcf.gz B.vcf.gz -R region.bed -n+1 -o tmp.vcf.gz -O z -c all -w1

 

Could anyone help?

Thanks a lot!

union bcftools vcf • 2.6k views
ADD COMMENTlink written 5.7 years ago by blueskypie50

1) Do you want to get sites that are common for A, B and region.bed? 

2) Or you want to merge A and B files and find common sites with region.bed?

3) And find A sites that are common for B and region.bed?

ADD REPLYlink written 5.3 years ago by Evgeniia Golovina1.0k
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