Question: Hello help for annovar..
1
gravatar for chanwoo1143
23 months ago by
chanwoo114310
chanwoo114310 wrote:

I need some help.. I have this . Using your resulting VCF determine 1) the number of single nucleotide variants, 2) the number of insertion/deletion variants, 3) the number of multi-necleotide variants, 4) the number of variants with multiple alternate alleles, and 5) the names of the 5 genes with the largest number of polymorphic sites.

I have my VCF file after using VCF filter. However, I am not sure how I can use annovar to do the task stated above.

This is my history https://usegalaxy.org/u/chawnerd/h/unnamed-history-1. This is urgent...

galaxy • 780 views
ADD COMMENTlink written 23 months ago by chanwoo114310
1

The ANNOVAR doc is at http://annovar.openbioinformatics.org/en/latest/. How far did you get before you got stuck? Specific details would be most helpful.

And, if you think it's an ANNOVAR specific question, you can post your question (with as much detail as possible) to the ANNOVAR mailing list: https://groups.google.com/forum/#!forum/annovar

ADD REPLYlink written 23 months ago by Dave Clements ♦♦ 2.3k

https://usegalaxy.org/u/chawnerd/h/unnamed-history-1 is the history; there are three gene sets one from mom, one from dad, and one from daughter. I need to find the SNPs from the reference genome homo sapiens hg 19. I am a bit kinda clueless how to proceed or if I have done these works correctly.

ADD REPLYlink written 23 months ago by chanwoo114310
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