Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Feedback on SNP filtering step before running PSMC fcr Bioinformatics 0 02-12-2013 03:41 AM
SNP filtering gfmgfm Bioinformatics 8 02-03-2013 10:01 AM
SNP filtering with vcftools tnguyen Bioinformatics 0 08-10-2012 04:05 AM
Ideal params for filtering SNP and Indels meher Bioinformatics 1 07-20-2012 01:54 AM
Maq SNP filtering script bug? qiudao Bioinformatics 9 03-03-2009 01:48 PM

Thread Tools
Old 04-09-2013, 10:01 AM   #1
Location: Moon

Join Date: Apr 2011
Posts: 60
Default SNP filtering

I had a list of interesting SNPs from tumor samples, I am wondering how I can remove the SNP associated with population identified through HapMap or 1000 Genomes. I would like to pick one of the following two ways:
1) filter dbSNP131 and 1000 Genome using annovar;
2) filter dbSNP or 1000 Genome SNPs using BedTools to filter UCSC dbSNP 137.
After filtering, almost nothing left, the left SNPs should be high-confidence, right?
lewewoo is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:59 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO