Calculate LD score using gnomAD matrices

Hail Query & hailctl
1

Hello,
I’m trying to calculate the linkage disequilibrium score (calculated by summing the LD values between the variant of interest with all other variants in a genomic region) using the gnomAD LD matrices (containing only LD values between all variants in BlockMatrix format) as well as the accompanying variant indices (in Hail Table format, first 10 rows seen below).

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My plan was to:

  1. Filter the variant indices table down to the variant of interest and get corresponding indices for the BlockMatrix

  2. use the variant locus information on the variant of interest as well as the window size and minor allele frequency to obtain the indices for all other variants in the specified genomic region

  3. Use the indices obtained from step 1 and 2 in the BlockMatrix to calculate LD score

However I am not sure how to obtain the indices after I have filtered the table down. Any help is appreciated!