How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate

Question

[Sudhir Jadhao]

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

[reza.jabal]

Can you provide an instance of your second vcf?

[Sudhir Jadhao]

Thank you, Reza, for your time.

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

Format: https://ibb.co/eePB97

[WouterDeCoster]

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

Answer 1

[reza.jabal]

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!

[Sudhir Jadhao]

Thank you!! It's working.

[reza.jabal]

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