How to compare 2 VCF files
2
3
Entering edit mode
8.4 years ago
Parimala Devi ▴ 100

Hey,
I have 2 vcf files. I want to compare the two, and save the SNPs that are common to both in a separate file, also save SNPs that are present only in 2nd file in another file.
Which tool do I use for this?

Thank you,

Parimala

SNP vcf Tool • 33k views
ADD COMMENT
0
Entering edit mode

i have file with three coloumns first coloumn containing the frequency of scaffolds(i.e. in 2nd coloumn) . Therefore i want to filter the file with coloumn having high count number in new file..

Thanx

ADD REPLY
5
Entering edit mode
8.1 years ago
Pablo ★ 1.9k

You can use "SnpSift" (specifically "SnpSift concordance" command)

ADD COMMENT
2
Entering edit mode
8.4 years ago

There is a tool that does it for you. Actually it can do a lot more than comparing vcf files.

VCFtools

ADD COMMENT
0
Entering edit mode

Thanks! I'm using vcf-isec.

ADD REPLY
0
Entering edit mode

Great.

ADD REPLY

Login before adding your answer.

Traffic: 1419 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