Separating a region of the VCF file
1
0
Entering edit mode
20 months ago

Hi Dear All,

I'm trying to separate 5Mb to 10Mb region of my VCF file with vcftools. But when I get the output, it only contains a header??

What is the best idea?

Codes I run:

 vcftools --vcf My_Chr20.vcf --chr 20 --from-bp 5000000 --to-bp 10000000 --recode --out My_Output

or 

 vcftools --vcf My_Chr20.vcf --chr 20 --from-bp 5000000 --to-bp 10000000 --recode  --recode-INFO-all --out My_Output

Best Regard

SNP VCFtools • 552 views
ADD COMMENT
0
Entering edit mode
20 months ago
ATpoint 48k

Use tabix and please use the search function next time:

Extract Sub-Set Of Regions From Vcf File

ADD COMMENT

Login before adding your answer.

Traffic: 1060 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6