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Build PRG from MSA and more sparsely from VCF #130

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ffranr opened this issue Jun 7, 2018 · 4 comments
Open

Build PRG from MSA and more sparsely from VCF #130

ffranr opened this issue Jun 7, 2018 · 4 comments
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@ffranr
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ffranr commented Jun 7, 2018

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@bricoletc bricoletc changed the title Build PRG from MSA Build PRG more flexibly and more inclusively Jun 14, 2019
@bricoletc
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bricoletc commented Jun 14, 2019

Targets here:

  1. We want to be able to build a PRG from a MSA right now

  2. Long alleles might need to be collapsed down. For eg a record of TCAGA (ref) and TTACA (alt) will 'overlap' any other variation within the same region. This creates combinatorial explosion (vcf_clusterer module) or straight out ignoring (perl script). One solution is building a graph from vcf and parsing that into a prg (this will collapse the SNPs in the long record); another (non-exclusive) is to allow nesting in gramtools, such that overlapping records are no longer flattened into one.

@bricoletc bricoletc changed the title Build PRG more flexibly and more inclusively Build PRG from MSA and more sparsely from VCF Jul 16, 2019
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Now that gramtools supports prgs made with make_prg, we need a streamlined way to build a whole-genome graph from:

  • a ref genome
  • a set of MSAs (as a fofn for eg)
  • a BED file (or equivalent) describing the MSA coordinates

From this gramtools (or make_prg?) runs make_prg on each MSA and combines the PRGs with the rest of the genome.

@kdm9
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kdm9 commented Feb 1, 2022

Hello folks,

I'm in the situation of needing exactly what @bricoletc describes above. Is there an approach that exists today which implements this functionality? Is this a serious plan with someone working on this functionality? If not, can I be of any assistance in making this a reality?

Best,
Kevin

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Hi @kdm9 , this is a timely question!
The feature is not currently implemented in a simple way at all, I've done it via a snakemake worfklow.
I will aim to implement this in gramtools. It should not be too complicated and is essential for tool usability. I estimate 2 weeks.

However, could you give me a sense of what you're trying to do? This would help make sure we're on same page and get a sense of your timeline. Feel free to drop email at [email protected] (also let me know if #163 works for you)

bricoletc added a commit that referenced this issue Feb 15, 2022
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