Parse_locus() over multiple regions using GRCh38

[lindsayvm]

Hi,

my data is on GRCh38 and I want to filter a set of SNPs from this. Im am looking for something like this:

intervals = [hl.parse_locus(x, reference_genome='GRCh38') for x in ['4:144585304', '15:78575140']]
mt_hits = hl.filter_intervals(mt, intervals, keep = True)

which is giving the error: TypeError: filter_intervals: parameter ‘intervals’: expected expression of type array<interval>, found list: [<LocusExpression of type locus>, <LocusExpression of type locus>]

[tpoterba]

In 0.2.15 or later, doing the following:

intervals = [hl.parse_locus(x, reference_genome='GRCh38') for x in ['4:144585304', '15:78575140']]
mt_hits = mt.filter_rows(hl.literal(intervals).contains(mt.locus))

will have the same performance as filter_intervals, but is much easier to use. See here:

New optimizer pass that extracts point queries and interval filters

hl.filter_intervals is one of the best ways to speed up pipelines that only need to look at a small fraction of your data, but the method is quite a pain to use compared to simpler methods like filter_rows. As of 0.2.15, Hail includes an optimizer pass that tries to rewrite filter / filter_rows method calls as filter_intervals when possible. This can make pipelines orders of magnitude faster, since it reduces the amount of data read from disk – and data you don’t read can’t slow you down! You’l…

[lindsayvm]

Thank you, I am now using HAIL version 0.2.15-652d93ae3419, but get this error:
Error summary: HailException: Invalid locus ‘4:144585304’ found. Contig ‘4’ is not in the reference genome ‘GRCh38’

I have also tried other loci of which I am also sure the should be in GRCh38, but all give the same error.

[tpoterba]

chromosome 4 is identified as chr4 in GRCh38

[lindsayvm]

Works! Thanks