SEQanswers

Go Back   SEQanswers > Applications Forums > Genomic Resequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
more precision about VarScan somatic Jane M Bioinformatics 35 09-14-2017 02:59 PM
Somatic Mutations in dbSNP qqcandy Bioinformatics 14 07-27-2015 02:34 PM
Pipeline to find somatic mutations david.tamborero Bioinformatics 6 08-09-2013 02:05 AM
Somatic SNP wanguan2000 Bioinformatics 2 03-13-2012 07:59 PM
Option "calmd"; Reporting indels and Somatic mutations for Whole Exome Seq data: angerusso Bioinformatics 0 01-10-2012 03:32 PM

Reply
 
Thread Tools
Old 10-07-2011, 01:46 AM   #1
Sam64
Member
 
Location: Paris

Join Date: Jun 2011
Posts: 15
Default Samtools mpileup_Paired Tumoral / Germline_keep only somatic mutations

I performed a genomic capture (Agilent technologie, SureSelect Target Enrichment System for Illumina Paired-end Sequencing) with paired tumoral and constitutional DNAs.
I created a .bam file for each both. I used bwa for alignment and samtools to create my bam file.
Now, I would like to call somatic mutations from these pair of samples (Tumoral vs Germline) with samtools (example of commands : samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf ). The goal is to eliminate all the commons mutations present in the two samples in order to keep only the somatic mutations.
Anybody can help me to understand how to realize this step?
What is the command for samtools ?
Thank you very much for your help
Sam64
Sam64 is offline   Reply With Quote
Old 12-29-2011, 09:29 AM   #2
david.tamborero
Member
 
Location: spain

Join Date: Feb 2011
Posts: 60
Default

did you check VarScan? It declares somatic state for each SNP/indel and provides some nice statistics by inputting the pileup files of the tumor/normal samples.
david.tamborero is offline   Reply With Quote
Old 02-29-2012, 11:01 AM   #3
dkoboldt
Member
 
Location: St. Louis

Join Date: Mar 2009
Posts: 62
Default

Sam64, it sounds like VarScan might be better suited to your needs.

Homepage: http://varscan.sourceforge.net

Download: https://sourceforge.net/projects/varscan/files/

Method Overview: http://varscan.sourceforge.net/somatic-calling.html
dkoboldt 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 11:44 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO