Closed floutt closed 1 year ago
Hi Tosin,
Thanks so much for your inquiry. In terms of the sparsity of Hail's BlockMatrix, please refer to the documentation here.
Briefly,
BlockMatrix.sparsify_row_intervals
(window around variants) and BlockMatrix.sparsify_triangle
(only upper triangular matrix is kept).BlockMatrix.from_numpy
(in-memory numpy object) and BlockMatrix.fromfile
(a binary file), I'd recommend recomputing a LD matrix in Hail. If you have a vcf file, you can hl.import_vcf
to make Hail MatrixTable, convert it to Hail BlockMatrix, and do linear algebra to compute LD.custom-ld-variant-index-path
represents a path to a Hail Table that records indices of variants in Hail BlockMatrix (required fields are shown below). custom-ld-label
is just an output label for the output. For example, if you specify custom
, the output contains a column custom_lead_r[2]
----------------------------------------
Global fields:
None
----------------------------------------
Row fields:
'locus': locus<GRCh38>
'alleles': array<str>
'idx': int64
----------------------------------------
Key: ['locus', 'alleles']
----------------------------------------
Hope this helps!
Best, Masa
Yes, thank you! This has been pretty helpful. I'll let you know if I have any more questions
I was able to run the software successfully with some modifications. This issue can be closed now. Thank you!
Hello!
Based on the documentation of this software I am aware that it is possible to run this QC pipeline with a user defined LD reference. Looking through the code, it looks like this argument requires that it be saved as a Hail BlockMatrix object. However, looking further into the code, it looks as if, in addition to this, the software requires additional
custom-ld-variant-index-path
andcustom-ld-label
parameters. The nature of these are a bit more vague.I have a few questions regarding all of this
1) I would like to build a sparse BlockMatrix object from our LD panel, is this software compatible with both sparse and dense BlockMatrix objects? 2) What would be a good way of building a sparse block matrix from a key-value R matrix pairing? I'd rather not build a dense matrix and sparsify it due to memory restrictions. 3) what is the nature of the
custom-ld-variant-index-path
andcustom-ld-label
parameters? How would one go about building them given an LD BlockMatrix?Cheers,
Tosin