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Please use taffy for subsetting and querying MAF files. It's included in the Cactus releases (binary or docker) if you don't want to build it yourself.
maf2hal doesn't scale very well and is used mostly for tests -- you are better off dealing directly with the MAF than converting to HAL.
Hi,
I am trying to use available MAF files from UCSC (by chromosomes) to extract some information.
It is unclear to me what I should do to:
I though I should use the maf2hal with the --refGenome mm10 for each chromosomes and then the halExtract listing the names but I am having issues.
Thanks for the help
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