How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
1
0
Entering edit mode
5.0 years ago

Hello Everyone,

I want to extract common SNP between two vcf files:

vcf1: hg19 genomic co-ordinate

vcf2: Refseq/LRG cDNA co-ordinate.

To get common vcf between these files. I need to convert hg19 genomic co-ordinate to LRG/RefSeq cDNA co-ordinate.

Can anyone please suggest me how to convert hg19 genomic co-ordinate to LRG/RefSeq cDNA co-ordinate?

Thak you in advance

snp • 1.4k views
ADD COMMENT
0
Entering edit mode

Can you provide an instance of your second vcf?

ADD REPLY
0
Entering edit mode

Thank you, Reza, for your time.

Actually, I have data in below format, not in VCF

Format: https://ibb.co/eePB97

ADD REPLY
0
Entering edit mode

See this post on how to add images to a post: [WorkInProgress]How to add images to a post

ADD REPLY
2
Entering edit mode
5.0 years ago
reza.jabal ▴ 570

Through two steps you can achieve this:

(1) Convert your cDNA nucleotide change to genomic coordinates using TransVar and generate a VCF file according to the hg19 assembly.

(2) Use GATK VCF union module or vcftools to identify common variants between the two files!

Hope it helps!

ADD COMMENT
0
Entering edit mode

Thank you!! It's working.

ADD REPLY
0
Entering edit mode

You're welcome! Can you please also accept the answer so it will be added to the resolved list.

ADD REPLY

Login before adding your answer.

Traffic: 1298 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