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lh3 / dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies
MIT License
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Reducing alignment size #2

Closed malmarri closed 3 years ago

malmarri commented 3 years ago

Hi

From the README:

"A raw variant call is made in the VCF if a non-reference allele is observed in any alignments >=50kb and mapped with mapping quality >=5."

Is it possible to have an option to reduce the alignment length like in paftools call -L?

Thanks

lh3 commented 3 years ago

Not possible at the moment. The threshold is hard coded. Dipcall is generally designed for high-quality assemblies. The contig N50 needs to reach a few megabase at least.