SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SNP base calling shuang Bioinformatics 7 10-24-2011 12:50 PM
Editing fasta , reference base in snp calling samtools moriah Bioinformatics 2 08-10-2011 12:11 AM
base composition and base calling arolfe Illumina/Solexa 2 07-29-2011 08:50 AM
tools for SNP calling in pooled samples gfmgfm Bioinformatics 0 12-30-2010 10:57 AM
SNP calling software in pooled samples mrxcm3 Bioinformatics 3 11-03-2010 10:38 PM

Reply
 
Thread Tools
Old 09-07-2011, 09:31 AM   #1
shuang
Senior Member
 
Location: IL

Join Date: Jul 2011
Posts: 100
Default SNP base calling for multiple samples

My goal is to find SNPs from multiple Sanger sequences, which cover varied regions, not necessary the same fragments. When a SNP is found, I want to see the base (or hetero/homo-zygote) of any samples which cover that position. What kind of software should I use? I would prefer a command-line software.


I tried to align sequences via bwasw and pileup all via samtools. However, when I pileuped all samples together, the output did NOT clearly distinguish between when a SNP location not covered in a sample and when a sample had hetero in that SNP location. My commands below.


samtools mpileup -uf Sorbil.fasta a1.bam a2.bam a3.bam | bcftools/bcftools view -bvcg - > raw.bcf

bcftools/bcftools view raw.bcf | vcfutils.pl varFilter -D100 > flt.vcf
shuang is offline   Reply With Quote
Old 09-07-2011, 10:44 AM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

I'm not sure what you mean by "clearly", but you should see a 1/1, 0/1 or 0/0 in each entry. That tells you if the SNP is predicted to be homozygous alternate, heterozygous, or homozygous reference. Unfortunately, what you really want is the DP4 for each sample separately, and doing a multi-vcf with samtools won't do that. You'll need the individual vcf file to see that.
swbarnes2 is offline   Reply With Quote
Old 09-07-2011, 03:06 PM   #3
shuang
Senior Member
 
Location: IL

Join Date: Jul 2011
Posts: 100
Default

In my case, some sequences showed 1/0 for a SNP position, however, some of those sequences did not cover that position.

I want to know whether a SNP base is a polymorphic, or wide type, or uncovered in a given sequence/file.
shuang 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 10:30 PM.


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