[Feature request] score many set of variants in a single pass

[wavefancy]

Dear Christopher,

Thanks much for developing and maintaining this great software. Can I ask for a new feature for the --score function.

Now it supports in a single pass score the same set of variants with different weights, each weight in a single column. However, can you please support score different sets of variants with different weights in a single pass? Probably, we can make a superset of variants and set some variants with 0 weight to have the same results in the current setting. However, if we want a gene-specific score for every gene, then the file will end up have more than 20000+ columns with many cells as zero. It looks very inefficient for computing. I may suggest a file with 20000+ rows, each row is a gene and list of variants with its weight associated, then the scoring only needs to load the necessary variants.

I think this feature would be very helpful for the rare variant association test, as you know, the burden score of each gene/or region is actually the sum of weighted scores. But calculate the score are very time consuming for many software, especially based on the input as vcf format. I think leverage on the plink and file format infrastructure, we can have the burden score very fast.

Thank you very much for your help.

Best regards Wallace

[chrchang]

Yes, it shouldn't be difficult to add support for a sparse input format to --score; I'll look into implementing this over the next week.

[wavefancy]

This is great, thank you very much for the support.

Best regards Wallace

[chrchang]

It isn't that much better than a bash for-loop, but --score-list exists, so I'll close this issue.