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Old 07-23-2015, 12:52 PM   #1
Amirj
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Location: Iran

Join Date: Jul 2015
Posts: 2
Default how to comare single variance with vcf file?

Hi,

Please check the problem and the solutoin I apply and tell me if it is correct or not.
The problem:
I have a few variances (chr,position,ref_base,alt_base,gene) and also 50 vcf files. I need to check that if my variances exist in any of VCF files.
The solution:
First I use Annovar program to convert vcf files to Annovar Input file (convert2annovar command) and second I user Annovar again (table_annovar command with refGene,esp6500siv2_all,1000g2014oct_all and snp138 protocols) to generate a tab delimited file which contain VCF variances and Lastly I user linux "cat" command and pipe in into "grep" command to check if any of my variaces exist in that annovar output file.

please tell that if this is a common way for searching a varince in a vcf file ?
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