Combining scans

Hail Query & hailctl
1

Hello again!

I’m having some trouble combining one scan annotation with another. I’ve created one scan on a table and would like to use that first scan to create a second one:

context_ht = context_ht.annotate(
    variant_count=hl.scan.group_by(
        context_ht.grouping,
        hl.scan.count()
    )
)
context_ht = context_ht.annotate(
    mu_agg=hl.scan.group_by(
            context_ht.grouping,
            hl.or_missing(
                hl.len(context_ht.variant_count) > 0,
                hl.scan.sum(
                    context_ht.mu_snp * context_ht.variant_count[context_ht.grouping]
                ),
            )
        )
)

image
image1344×404 26.2 KB

I’d like to use variant_count to create a new scan annotation but keep running into this error:

Error summary: HailException: Key 'ACA-C-T-0-false-70'    not found in dictionary. Keys: []

Am I not skipping the first line of the table correctly? Is there a better way to combine these scans?

2

My guess is because the scan is not inclusive of the line you’re in? If you trust that it should always be there, you could context_ht.variant_count.get(context_ht.grouping, 0) maybe (default to 0 if not seen yet)?

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