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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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Flag samples with insertions #135

Open donkirkby opened 10 years ago

donkirkby commented 10 years ago

E-mail request from Richard H. Put this flag in the sample header of the consensus sequence download file? Which kind of insertions: relative to coordinate reference, relative to consensus, or both?

ArtPoon commented 9 years ago

Consensus sequence contains insertions already. Insertions relative to sample consensus would not appear, remains a potential issue. Follow up with RH on indel polymorphisms relative to sample consensus.