Question: How to further process and annotate VCF files derived from mapping a patient`s whole genome FASTQs to a separate genes GenBank (.gbk) files?
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gravatar for mathisdead
6 months ago by
mathisdead0
mathisdead0 wrote:

How to further process and annotate VCF files derived from mapping a patient`s whole genome FASTQs to a separate genes GenBank (.gbk) files? I have genome of a patient having medullary thyroid cancer. I have run alignment to a set of 30 genes relevant to cancerogenesis and chemotherapy decision. Some genes have a few mutations, some over a 1000 of them. Now I have 30 VCF files and .csv SNP and INDEL lists. I need to know what to do with these files: should i put them into SNPEfff or there is some proper web service to do annotation? In other words, What processing steps are to be done with these VCF files, is it necessary to filter them, normalize or smth else? Never had an experience with an actual human genome before

ADD COMMENTlink modified 6 months ago • written 6 months ago by mathisdead0

Why do you want genbank format?

ADD REPLYlink written 6 months ago by WouterDeCoster32k

I used that format for references only. No matter what format I will get on annotation. thx.

ADD REPLYlink written 6 months ago by mathisdead0

So you can just annotate your vcf files using Snpeff, annovar or VEP, right? Or did I misunderstood your question?

ADD REPLYlink written 6 months ago by WouterDeCoster32k

Thx. Can I use wANNOVAR or the other web service?

ADD REPLYlink written 6 months ago by mathisdead0

I haven't used those, but should work.

ADD REPLYlink written 6 months ago by WouterDeCoster32k
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