Question: SnpEff html and .vcf file result are not matching
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gravatar for misbahabas
2.0 years ago by
misbahabas60
misbahabas60 wrote:

Asslamu Alikum

I have successfully managed to run SnpEff for my vcf files. However, the count of missense variants in my html file and the VCF file generated by SnpEff are different.

Missense in HTML: 20,854

Missense in VCF fle: 20,754

Can any one please suggest me about the criteria for missense calculation in html file, so that I could match the vcf file with the missense file

Input used is vcf and version SnpEff 4.3

snp tool snpeff vcf • 865 views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.0 years ago by misbahabas60

If any one know about it please tell me i am in trouble

ADD REPLYlink written 2.0 years ago by misbahabas60

Have you visually checked the VCF and HTML files to see where they differ? That is where I would start. For example, take the first variant position from your VCF and then search for it in the HTML. If you see find it more than once, you may then become enlightened as to what has happened.

My guess is that the discrepancy has something to do with transcript isoforms. In that sense, it will help to see the exact command that you used for SnpEff.

Thanks! Kevin

ADD REPLYlink written 22 months ago by Kevin Blighe46k
1

Thanks kevin ,

i had solved this problem because some issues was in my vcf

ADD REPLYlink written 21 months ago by misbahabas60
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