Export consensus sequence from IGV

[Yue Ying]

Hi all, 

I would like to know if it is possible for me to export the consensus sequence after I have aligned the BAM files onto the reference genome on IGV. I just wish to export a particular region of interest. If IGV does not have this feature, any idea what are the other alternatives I can use? Something more friendly for biologist perhaps?

Thanks and looking forward to your reply soon.

Cheers,

Yue Ying

[Jim Robinson]

Hi Yue,

Apologies for the delayed reponse.  IGV does not compute a consensus sequence,  there are tools for that but I am not sure they qualify as biologist friendly.   I think the GATK and samtools should be able to do this, perhaps one of the Picard tools.

Jim

[Jacob Silterra]

Hi Yue,

Just an FYI, you can now export the consensus sequence from a BAM file in the latest release of IGV. See the documentation of AlignmentTrack popup menu, under "Copy consensus sequence"

Thanks,

-Jacob

--
 

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
Jacob Silterra
Software Engineer
Broad Institute

[Yue Ying]

Hi Jacob,

Thank you very much! Exactly what I was looking for! 

Cheers,

YueYing

--
 
---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/-49NnJuy-s4/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

For more options, visit https://groups.google.com/groups/opt_out.

--
Best regards,
Yue Ying

[thyss...@gmail.com]

Hi Jacob,
How do I "paste"?
I am running linux.
I right click on the reads track, select "copy consensus"
When I switch into my text editor, there is nothing to paste.
Thanks,
Greg

[Jacob Silterra]

Hello,

The consensus sequence gets copied to the system clipboard. There should be a paste option in the edit menu of your text editor, or else ctrl+v is the standard keyboard shortcut.

-Jacob

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/7c32c3c8-a575-4980-9062-af7ea2583387%40googlegroups.com.

For more options, visit https://groups.google.com/groups/opt_out.

[Dr. Thyssen]

This works on my windows machine, but not on my linux box.  I run RHEL6.0

Could this be an OS specific bug?

Does it work for you on linux?
Thanks,
Greg

--
 
---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/-49NnJuy-s4/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAFbhPKUgd3wogRAFZdsO%3DBpGNQojpFJNa09%3DFQWSwuNUMUKh3A%40mail.gmail.com.

[Jacob Silterra]

We don't have a RedHat linux machine to test it on. I've tested on Ubuntu Linux and it works fine. It certainly could be OS-specific.

-Jacob

[Monique]

Hi 

Is it possible to export the consensus sequence from the command line? I have a bunch of bam files that I want to export the consensus from a particular region in the files. I can do this one at a time using the IGV GUI but I would much prefer to automate this process.

-I have had a look at the manual, but I can't see an export consensus option in the command line

Thanks

Monique

[Jim Robinson]

Hi,

We don't have that option at the moment, this is the type of analysis
we normally leave for analysis programs like samtools. Have you explored
other command line options (e.g. samtools or picard). This is not an
area I'm familiar with, so I'm not sure what's already out there.

Jim

[Andrew Farmer]

Hi-
vcftools has a vcf-consensus program which may be close to what you're
looking for; you'd
have to call variants from your bam files first, though.

hope that helps

Andrew

[Monique]

Hi 

I am familiar with samtools but for some reason mpileup doesn't produce anything meaningful (despite me being able to visualize many reads using IGV and extract the sequence).I am trying a slightly unorthodox approach at extracting a particular gene from my resequenced genomes (I have used samtools successfully across the whole genome though). I'll try samtools again and see if I can get it to work.

Thanks!

Monique

[Jim Robinson]

If you can't, or if there really isn't an easy-to-use alternative I will look into adding this to igvtools.   Be aware however that this isn't our expertise, we implemented the algorithm in the paper cited but our knowledge of this subject ends there.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/6b53b348-9fa5-4fa3-9bc3-e89fe6e2cd3f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Monique]

Hi Jim

I'll see how I go, I tested this approach on a few samples, I'll see if samtools works better when I increase the number of individuals. In this case I'm more interested in a presence/absence of a particular target gene so although the  SNP sites are  desirable they aren't essential. Thats why the IGVtools copy consensus sequence approach is ok.  If I can't get this to work in any other way I'll contact you again.

Thanks

Monique