Question: How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
0
gravatar for Sudhir Jadhao
2.2 years ago by
India
Sudhir Jadhao70 wrote:

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 • 571 views
ADD COMMENTlink modified 2.2 years ago by reza.jabal370 • written 2.2 years ago by Sudhir Jadhao70

Can you provide an instance of your second vcf?

ADD REPLYlink written 2.2 years ago by reza.jabal370

Thank you, Reza, for your time.

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

Format: https://ibb.co/eePB97

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Sudhir Jadhao70

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

ADD REPLYlink written 2.2 years ago by WouterDeCoster44k
2
gravatar for reza.jabal
2.2 years ago by
reza.jabal370
New York, USA
reza.jabal370 wrote:

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 COMMENTlink modified 2.2 years ago • written 2.2 years ago by reza.jabal370

Thank you!! It's working.

ADD REPLYlink written 2.2 years ago by Sudhir Jadhao70

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

ADD REPLYlink written 2.2 years ago by reza.jabal370
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