How do I export consensus sequence from IGV?

Bean · 08-19-2010, 05:21 AM

Hi all,

not sure where to post this, so I'll put it under general.

I am checking sequences (bam files) with the IGV genome viewer, and can't figure out how to export a consensus sequence for regions containing SNPs. If I use the "define a region of interest/copy sequence" button, it copies the reference sequence for that region, not the consensus.

Is this possible in IGV; if so, how do I do that? If not, can anyone recommend a (free) bam-file viewer in which one can define (SNP threshhold etc.) a consensus and export that as a fasta or simple textfile?

Thanks in advance!

Greets
Bean

Jim Robinson · 08-30-2010, 03:06 PM

Hi Bean,

I'm the developer of IGV. You are correct you cannot do that in IGV, but it looks like a useful feature to have. I'm a little unclear on the snp threshold setting, if you want to email me with details at igv-help@broadinstitute.org I'm sure we can add this feature. You can post it here as well, but the email above comes directly to me, some days I'm too busy to check the message boards!

Regards,

Jim

shangool · 09-09-2010, 08:51 AM

HI
I have the same problem now, that I should look at my cosensus seq. I already get my consensus file from samtools, but I do not know how I can convert it fastq from pileup, because I have BLAST these consensus seqs.
Many tanks

sadiexiaoyu · 06-17-2013, 01:45 AM

Quote:

Originally Posted by Bean

Hi all,

not sure where to post this, so I'll put it under general.

I am checking sequences (bam files) with the IGV genome viewer, and can't figure out how to export a consensus sequence for regions containing SNPs. If I use the "define a region of interest/copy sequence" button, it copies the reference sequence for that region, not the consensus.

Is this possible in IGV; if so, how do I do that? If not, can anyone recommend a (free) bam-file viewer in which one can define (SNP threshhold etc.) a consensus and export that as a fasta or simple textfile?

Thanks in advance!

Greets
Bean

Hi, Bean,

Three years later

Have you found anyway to solve this problem? I am also interested in how to use IGV to export consensus sequence. Thanks!

Best,

Sadiexiaoyu

Jim Robinson · 06-17-2013, 07:04 AM

Hi,

This is not something IGV currently does. As you can see from my last post I'm not clear on the specifics of how a consensus sequence is defined, other than as a pileup. Some decision needs to be made re a call for each base, perhaps using ambiguity codes when a call cannot be made. If you want to help us develop some simple rules we will consider implementing it. This is better done in the igv-help google group, where other IGV users and contributors can participate.

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08-19-2010, 05:21 AM	#1
Bean Junior Member Location: Germany Join Date: Apr 2010 Posts: 8	How do I export consensus sequence from IGV? Hi all, not sure where to post this, so I'll put it under general. I am checking sequences (bam files) with the IGV genome viewer, and can't figure out how to export a consensus sequence for regions containing SNPs. If I use the "define a region of interest/copy sequence" button, it copies the reference sequence for that region, not the consensus. Is this possible in IGV; if so, how do I do that? If not, can anyone recommend a (free) bam-file viewer in which one can define (SNP threshhold etc.) a consensus and export that as a fasta or simple textfile? Thanks in advance! Greets Bean

08-30-2010, 03:06 PM	#2
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Hi Bean, I'm the developer of IGV. You are correct you cannot do that in IGV, but it looks like a useful feature to have. I'm a little unclear on the snp threshold setting, if you want to email me with details at igv-help@broadinstitute.org I'm sure we can add this feature. You can post it here as well, but the email above comes directly to me, some days I'm too busy to check the message boards! Regards, Jim

09-09-2010, 08:51 AM	#3
shangool Junior Member Location: Austria Join Date: Aug 2010 Posts: 5	HI I have the same problem now, that I should look at my cosensus seq. I already get my consensus file from samtools, but I do not know how I can convert it fastq from pileup, because I have BLAST these consensus seqs. Many tanks

06-17-2013, 07:04 AM	#5
Jim Robinson Member Location: Boston, MA Join Date: May 2009 Posts: 75	Hi, This is not something IGV currently does. As you can see from my last post I'm not clear on the specifics of how a consensus sequence is defined, other than as a pileup. Some decision needs to be made re a call for each base, perhaps using ambiguity codes when a call cannot be made. If you want to help us develop some simple rules we will consider implementing it. This is better done in the igv-help google group, where other IGV users and contributors can participate.