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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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specifying a bed interval file for halSnps #270

Closed tli71193 closed 1 year ago

tli71193 commented 1 year ago

Hi there,

I am wondering if I can specify regions in the reference genome in halSnps rather than go through the entire reference genome to speed things up.

I see there's an argument --start that may be an option to use but how can i specify an interval rather than the chromosome?

this may be a simple question and maybe I'm just very clueless in knowing how to use the function.

Thanks in advance for the help!

diekhans commented 1 year ago

you can use --refSequence, --start, --length to get a region.

It would be nice if this could be a ucsc/samtools style seq:start-end

Tony Li @.***> writes:

Hi there,

I am wondering if I can specify regions in the reference genome in halSnps rather than go through the entire reference genome to speed things up.

I see there's an argument --start that may be an option to use but how can i specify an interval rather than the chromosome?

this may be a simple question and maybe I'm just very clueless in knowing how to use the function.

Thanks in advance for the help!