Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
more precision about VarScan somatic Jane M Bioinformatics 35 09-14-2017 03:59 PM
Can VarScan be used to find out Somatic Mutations in RNA seq Data ? swapnil2188 RNA Sequencing 1 12-10-2012 08:13 AM
Patchwork - allele-specific somatic CNAs in cancer (WGS) mackan Bioinformatics 2 04-19-2012 05:54 AM
allele frequency threshold GATK m_elena_bioinfo Introductions 3 12-12-2011 12:29 PM
how to fetch the snp allele frequency? dzmtnvmt Bioinformatics 3 06-21-2011 04:44 AM

Thread Tools
Old 06-11-2012, 04:21 AM   #1
Location: Sweden

Join Date: Jan 2011
Posts: 12
Default how does varscan somatic compute variant allele frequency?

Dear all,

I wonder how "varscan somatic" computes the variant allele frequencies. Is it by simple counting the reference bases (".", ",") and variant bases in the tumor pileup file and dividing the read count for the variant by the sum? Is there any filtering of the bases involved, e.g. by base quality or read mapping quality? In the publication (Koboldt et al, Genome Research 2012), it is stated that varscan requires minimum phred base quality of 20. Is it being used for calling the variant as well as calculating allele frequency?

Thanks in advance for your reply.
genomicist 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 04:05 PM.

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