SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Why MAQ consensus seq better than SAMtools consensus ?? av_d Genomic Resequencing 5 10-18-2015 03:44 AM
How to make sense of Tophat's output file 'junctions.bed' gsinghal RNA Sequencing 4 09-03-2012 06:49 AM
Make Clean and Make all not working qnc Bioinformatics 27 10-21-2011 10:17 AM
how to make consensus call of diploid genotypes from bam file cindyz Bioinformatics 1 07-23-2010 03:32 PM
Can anyone make sense of the quality scores in the qseq.txt files? TylerBackman Bioinformatics 2 04-29-2009 09:23 AM

Reply
 
Thread Tools
Old 11-27-2012, 01:21 PM   #1
skblazer
Member
 
Location: Massachusetts

Join Date: Feb 2009
Posts: 50
Default Consensus genotypes of SOAPsnp make no sense

Hello,

Is there anyone familiar with soapsnp? I tried soapsnp recently for SNP calling, but cannot get any SNP calls. All of the candidate variants were not called. I cannot understand why below sites, for example, were reported as REF genotypes, considering the depth and quality are both good. I also tried feeding with different -r and -e, but similar result was generated.


chr1 204115 A A 0 T 34 2 2 A 34 2 2 4 1.00000 1.00000 0
chr1 204253 A A 0 G 38 17 17 A 0 0 0 17 1.00000 1.00000 0
chr1 206781 A A 0 T 38 18 18 A 0 0 0 18 1.00000 1.00000 0
chr1 207116 G G 0 A 35 8 8 G 0 0 0 8 1.00000 1.00000 0
chr1 207206 G G 0 C 36 17 17 G 0 0 0 17 1.00000 1.00000 0
chr1 207274 G G 0 T 37 14 14 G 0 0 0 14 1.00000 1.00000 0

Best,
skblazer is offline   Reply With Quote
Reply

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 10:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO