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

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
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updated by reza.jabal reza.jabal • written by Sudhir Jadhao Sudhir Jadhao

Can you provide an instance of your second vcf?

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written by reza.jabal reza.jabal

1 answer

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!

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written by reza.jabal reza.jabal

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

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written by reza.jabal reza.jabal

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