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lh3 / dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies
MIT License
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Using winnowmap #12

Closed steven-solar closed 1 year ago

steven-solar commented 1 year ago

Attempted to run dipcall using winnowmap (by passing -W repetitive_k15.txt) and saw the following error in dipcall.hap1.paf.gz.log:

[M::mm_idx_gen::0.003*1.15] reading downweighted kmers
ERROR: input list of k-mers and winnowmap parameter k are inconsistent

My repetitive_kmer file is of the form:

CGGAATTGAATGGAA 18274
CTCAAAAACAAAAAA 4552
CGGAATTGAATGGAA 12469
...

Unless there is a way to pass a value for k to dipcall, what value of k does dipcall anticipate? I did not see it listed in the documentation, or in the error message. I know k=15 is the default for winnowmap, which is why I tried that first.

lh3 commented 1 year ago

You are doing assembly alignment. Winnowmap2 uses 19-mer by default.