Question: How to update hg19 vcf genomic co-ordinate to LRG/RefSeq cDNA co-ordinate
0
gravatar for Sudhir Jadhao
17 months ago by
India
Sudhir Jadhao60 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 • 401 views
ADD COMMENTlink modified 17 months ago by reza.jabal330 • written 17 months ago by Sudhir Jadhao60

Can you provide an instance of your second vcf?

ADD REPLYlink written 17 months ago by reza.jabal330

Thank you, Reza, for your time.

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

Format: https://ibb.co/eePB97

ADD REPLYlink modified 17 months ago • written 17 months ago by Sudhir Jadhao60

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

ADD REPLYlink written 17 months ago by WouterDeCoster41k
2
gravatar for reza.jabal
17 months ago by
reza.jabal330
New York, USA
reza.jabal330 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 17 months ago • written 17 months ago by reza.jabal330

Thank you!! It's working.

ADD REPLYlink written 17 months ago by Sudhir Jadhao60

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

ADD REPLYlink written 17 months ago by reza.jabal330
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