Does IGV support MAF multiple alignment format?

[Yury Bukhman]

Hi,

I am trying to visualize a multiple genome alignment. I have the alignment in MAF format. I have uploaded the reference genome from a FASTA file. Although IGV seems to load the MAF file, nothing is displayed. The only track I get is called Gaps, and it's empty.

Thanks!

Yury

[James Robinson]

It should work, but is rarely used.   The following MAF file works for hg18,  you might compare it to yours.  Download it,  load genome hg18,  load the MAF file from the File menu,  and jump to chr1:40,187-40,227.    https://raw.githubusercontent.com/igvteam/igv/master/test/data/maf/ucscSample.maf

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[Yury Bukhman]

Thanks, James! Your example works. My file was missing the first line, which specifies track name and species order. After adding that in, I can see the species tracks but they are still empty. If MAF is rarely used with IGV, I wonder if it's worthwhile to look into this further.

Is visualizing whole-genome alignments one of IGV's intended uses in the first place? If so, what is the best format to use? If not, are you aware of another tool I could try?

[James Robinson]

Visualizing sequence alignments in the form of BAM files is very common use of IGV.   You typically would start with a "SAM" text file, then create a binary BAM file from that.   Just google their are lots of resources on doing that,  samtools is often used.

What program created this MAF file?

On Tue, Dec 4, 2018 at 2:05 PM Yury Bukhman <yuryb...@gmail.com> wrote:

Thanks, James! Your example works. My file was missing the first line, which specifies track name and species order. After adding that in, I can see the species tracks but they are still empty. If MAF is rarely used with IGV, I wonder if it's worthwhile to look into this further.

Is visualizing whole-genome alignments one of IGV's intended uses in the first place? If so, what is the best format to use? If not, are you aware of another tool I could try?

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[Yury Bukhman]

The MAF file was generated from a HAL file using the hal2maf tool from Comparative Genomics Toolkit, https://github.com/ComparativeGenomicsToolkit/hal. The original HAL file was generated by the cactus whole genome aligner from a small example dataset provided for testing the software. I can upload it somewhere if you are interested.

[James Robinson]

I will look at it if you upload it,  also point me to the fasta.  

On Wed, Dec 5, 2018 at 7:23 AM Yury Bukhman <yuryb...@gmail.com> wrote:

The MAF file was generated from a HAL file using the hal2maf tool from Comparative Genomics Toolkit, https://github.com/ComparativeGenomicsToolkit/hal. The original HAL file was generated by the cactus whole genome aligner from a small example dataset provided for testing the software. I can upload it somewhere if you are interested.

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[Yury Bukhman]

James, you can get the files here: https://drive.google.com/drive/folders/1CVGxxKvNH-wiN8cbmvVdkUQTAtuneVgS?usp=sharing

Thanks!

Yury

[James Robinson]

OK, progress.  Some subtle differences in the HAL output and UCSC produced MAF files were tripping up the parser. 

I have you file working now, but I had a follow-on question.   At what genomic scale do you intend or hope to view this MAF file.   The track for this format is designed for very zoomed in views, at the level of base pair,  a few hundred bp width at most.   Is this what you envision?

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[James Robinson]

You can zoom back to about a kb with this format,  its designed primarily to highlight base mismatches between the alignments and a reference.

[Yury Bukhman]

Thanks, James! Could you send me the modified file?

Regarding your question, I would like to be able to look at different scales. I have alternative genome assemblies of the same species generated using different technologies. I am hoping to align them to each other and to supporting evidence, e.g. Illumina and PacBio reads, in order to examine the differences. I expect that some of the differences would be at base pair level while others at larger scales, e.g. alternative ordering of contigs, inversions etc. It looks like something other than IGV may be appropriate for the latter: I am thinking of the UCSC genome browser. I am a novice in this area, hunting for tools that might help me.

Yury

[James Robinson]

Hi Yury,

I didn't change you file,  I fixed the parser in IGV.   This will be included in the next point release, but you can get it now from the development snapshot builds:  http://software.broadinstitute.org/software/igv/download_snapshot

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[Yury Bukhman]

Hi James,

I have downloaded the snapshot but, in my hands, it still does not work. I still got empty tracks.

I have "Version snapshot 12/07/2018 01:36 AM"

Thanks.

Yury

[James Robinson]

Try deleting your "maf.index" file to force IGV to regenerate it

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[Yury Bukhman]

It works now! Regenerating the index worked. Many thanks!

Yury