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airr-community / ogrdb

Website and associated database for managing submissions of inferred alleles
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Add 'difference to cloest in host' fields to genotype summary #39

Closed williamdlees closed 5 years ago

williamdlees commented 5 years ago

Thanks Andrew. I'll add fields for nt and aa differences to the closest reference in host.

William On 15/03/2019 04:39, Andrew Collins wrote:

Hi William,

The 'nt diff' field in the Genotype table refers to differences between an inference and the closest reference germline gene. I think it would be informative to show differences with respect to the nearest reference sequence in the host.

This came to mind as I looked at an IGHV4-30-4 inference in S0009, where the nearest germline gene in the host is given as IGHV4-61. In order to understand whether or not misalignments of mutated sequences have led to these IGHV4-30-4 alignments, we need to know how this sequence relates to IGHV4-61.

williamdlees commented 5 years ago

Agreed on the IARC call today that we will add just the nt difference to the closest-in-host.