Entering edit mode
9.8 years ago
blueskypie
▴
70
I have the following files:
A.vcf
which contains one sample s1B.vcf
which contains one sample s1region.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!
0
Entering edit mode
- Do you want to get sites that are common for A, B and region.bed?
- Or you want to merge A and B files and find common sites with region.bed?
- And find A sites that are common for B and region.bed?
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updated 2.6 years ago by
Ram
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written 9.3 years ago by
Evgeniia Golovina
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