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cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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HLA-B exon 2 reference is not in correct frame #192

Closed ArtPoon closed 9 years ago

ArtPoon commented 9 years ago

Translated sequences should start GSHS

ArtPoon commented 9 years ago

Exons 2 and 3 are in different reading frames. Proposed fix: put a fake bp into nucleotide reference to enforce consistent reading frame. Instead, let's see if it helps if we just put in the correct AA coordinate reference for HLA B*57:01 in projects.json.

donkirkby commented 9 years ago

The new reference sequence for HLA B exon2 is too long, and doesn't seem to match the B57:01:01 reference from the [IMGT/HLA database](http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele.cgi?B57:01:01), so I'm reopening this issue.