SnpEff html and .vcf file result are not matching

Question

[misbahabas]

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

[misbahabas]

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

[Kevin Blighe]

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

[misbahabas]

Thanks kevin ,

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