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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Trying to run cactus-hal2maf with --refGenome Anc0 #1331

Closed BlackSlipper closed 3 months ago

BlackSlipper commented 3 months ago

Hi, I created a pangenome and got a HAL file.

i am trying to convert HAL file into MAF conserving all the non-reference alignments.

In this context, is it okay to use "cactus-hal2maf with --refGenome Anc0" option?

It says in the document that it is recommended to create the maf using the --noAncestors options with cactus-hal2maf.

What are the pros and cons of setting --refGenome Anc0 ?

glennhickey commented 3 months ago

most people don't want the ancestors in the maf, so that's why the --noAncestors is recommended. If you want non-reference sequence, --refGenome Anc0 is probably the best way. You probably want to go in afterwards and filter out blocks that do not align to any of your input genomes (ie that are just ancestor and minigraph) though. mafFilter may help you there. UPDATE: cactus-hal2maf may actually take care of this filtering for you by default.

BlackSlipper commented 3 months ago

Thank you! I appreciate your help