SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Somatic Mutations in dbSNP qqcandy Bioinformatics 14 07-27-2015 02:34 PM
Samtools mpileup - Call somatic mutations from a pair of samples - detail steps ? swapnil2188 General 2 09-23-2013 04:49 PM
Pipeline to find somatic mutations david.tamborero Bioinformatics 6 08-09-2013 02:05 AM
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 04-05-2012, 10:08 AM   #1
swapnil2188
Member
 
Location: Indianapolis

Join Date: Feb 2012
Posts: 12
Default Doubts regarding samtools mpileup - Call somatic mutations from a pair of samples ?

I am trying to compare two samples for somatic mutations using Samtools mpileup. (RNAseq data)


The two .bam files or samples I am comparing include multiple samples merged together into them (3 .bam files in one and 8 in other- merged using samtools merge)

The command given in the manual
( " samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf" ) doesnt specify the number of samples (inputs)

I used this command

samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair - > var.bcf

It gives me back the error saying
"[mpileup] 1 samples in 2 input files
<mpileup> Set max per-file depth to 8000
[afs] 0:0.000"

I also tried to make a sample.txt file for the two samples (merged files) and used this command

"samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf "

I still get an error (different error)

Is there anything wrong here ?

What should be the ideal steps to find out somatic variants between two samples ? (samples include multiple bam files merged together)

Please suggest me some steps to be followed in order to find out somatic variants by comparing two samples using samtools mpileup

Thanks!
swapnil2188 is offline   Reply With Quote
Old 04-09-2012, 12:14 PM   #2
swapnil2188
Member
 
Location: Indianapolis

Join Date: Feb 2012
Posts: 12
Default

Quote:
Originally Posted by swapnil2188 View Post
I am trying to compare two samples for somatic mutations using Samtools mpileup. (RNAseq data)


The two .bam files or samples I am comparing include multiple samples merged together into them (3 .bam files in one and 8 in other- merged using samtools merge)

The command given in the manual
( " samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf" ) doesnt specify the number of samples (inputs)

I used this command

samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair - > var.bcf

It gives me back the error saying
"[mpileup] 1 samples in 2 input files
<mpileup> Set max per-file depth to 8000
[afs] 0:0.000"

I also tried to make a sample.txt file for the two samples (merged files) and used this command

"samtools mpileup -DSuf ref.fa aln1.bam aln2.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf "

I still get an error (different error)

Is there anything wrong here ?

What should be the ideal steps to find out somatic variants between two samples ? (samples include multiple bam files merged together)

Please suggest me some steps to be followed in order to find out somatic variants by comparing two samples using samtools mpileup

Thanks!
Please can Anyone help me with this ?

I am waiting for response !

Thank You !
swapnil2188 is offline   Reply With Quote
Old 05-18-2012, 06:54 AM   #3
gaffa
Member
 
Location: Gothenburg/Uppsala, Sweden

Join Date: Oct 2010
Posts: 82
Default

Do you have read group information specified in the two files?
gaffa 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 03:12 AM.


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