Question: how to compare variances with VCF file ?
0
gravatar for amir.jebelli
3.9 years ago by
amir.jebelli50
Iran/Mashhad
amir.jebelli50 wrote:

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 ?

vcf • 1.1k views
ADD COMMENTlink modified 3.9 years ago by Sean Davis25k • written 3.9 years ago by amir.jebelli50
1

i think with VCFtools you can define and filter indels...az koja bioinformatics yad gerefti kalak?

ADD REPLYlink written 3.9 years ago by F3.4k
1

I use vcfinterset from vcflib to solve the problem. I also find that I can filter vcf files with vcftools program.

4-5 mahi hast khodam shoro kardam be yad gereftam.

ADD REPLYlink written 3.9 years ago by amir.jebelli50

eyval dadash, carry on

ADD REPLYlink written 3.9 years ago by F3.4k
2
gravatar for Sean Davis
3.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You might take a look at tools like bedtools, bedops, vcftools, or VariantAnnotation/GenomicRanges (Bioconductor).  

ADD COMMENTlink written 3.9 years ago by Sean Davis25k
1

Yup, one or more of these programs will allow the OP to do exactly what they want.

ADD REPLYlink written 3.9 years ago by Dan Gaston7.1k

Thanks Sean, I use vcfintersect from vcflib to check if my variances exists in vcf file.

vcfintersect -b MY_INPUT_VARIANCES.bed MY_VCF_FILE.vcf.gz
ADD REPLYlink written 3.9 years ago by amir.jebelli50
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