SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
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
Questions about pathway analyses of genes with somatic mutations alexbmp Bioinformatics 0 03-19-2012 06:41 PM
Samtools mpileup_Paired Tumoral / Germline_keep only somatic mutations Sam64 Genomic Resequencing 2 02-29-2012 11:01 AM
Samtools mpileup on multiple samples cristae8 Bioinformatics 6 01-27-2012 10:58 AM

Reply
 
Thread Tools
Old 03-26-2012, 12:19 PM   #1
swapnil2188
Member
 
Location: Indianapolis

Join Date: Feb 2012
Posts: 12
Default Samtools mpileup - Call somatic mutations from a pair of samples - detail steps ?

Can any one please clear some doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf

now I did get what each option means (DSuf...) but have doubts regarding others.

Now T stands for comparing two pair of samples for somatic variants but the syntax or the example command given only includes one.bam file.

Are we suppose to input two .bam files (files which need to be compared in order to find out somatic variants ?)

I used two bam files as input but it displays back the help menu again w/o any error been displayed. What can be the reason.

I have sorted and indexed the bam files (to be compared) already.
Is there something wrong with the command i used ?

What are the ideal steps to be followed for analysing somatic variants ?

Please can anyone help ?

Thanks !
swapnil2188 is offline   Reply With Quote
Old 05-13-2012, 11:49 PM   #2
bpetersen
Member
 
Location: Germany

Join Date: Mar 2010
Posts: 20
Default

I would also be interested in the exact steps to use for finding somatic mutations with samtools, any new insights yet?
bpetersen is offline   Reply With Quote
Old 09-23-2013, 04:49 PM   #3
sophiespo
Member
 
Location: australia

Join Date: Apr 2013
Posts: 15
Default

Sorry to resurrect an old thread but I am also trying to figure this out.

samtools mpileup -DSuf ref.fa tumor.bam normal.bam | bcftools view -bvcgT pair - > var.bcf

This gives me mutations that are in both bam files. But I am only interested in mutations in the tumor and not the normal.

I have also performed separate analyses on each sample and then subtracted the normal from the tumor but this is not regarded as the best way to do things these days.

Ideas?
sophiespo 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 03:59 PM.


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