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nlesc-ave / ave-rest-service

visualize (clustered) single-nucleotide variants across genomes
Apache License 2.0
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dont ignore heterozygosity variants #24

Closed sverhoeven closed 6 years ago

sverhoeven commented 7 years ago

Map the alts to a ambiguous bp using http://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html

sverhoeven commented 7 years ago

Fixed in 6cf681e4d0e5e399b362e42faafffcb6e425cc52

sverhoeven commented 7 years ago

Applied wrong heterozygous detection. See https://www.biostars.org/p/119731/

sverhoeven commented 7 years ago

We need to map genotype of each sample to the alts. See https://github.com/nlesc-ave/ave-rest-service/blob/e51a3645f789b80d4a9a0de25a551f82fb4d4ff1/avedata/variants.py#L115-L118 for implementation.

Next up, propagate the nucleotide of variant+sample to haplotype cluster. This requires changein app see https://github.com/nlesc-ave/ave-app/tree/ambigous-genotype