diff --git a/README.md b/README.md index 1b2d6e6239dbf34588c8ea444151e0ecd953c3e7..70ee6a10f04be92a405b66b866df98dac3f97507 100644 --- a/README.md +++ b/README.md @@ -199,6 +199,11 @@ Hub-CDB and Institut Pasteur <br /><br /> ## WHAT'S NEW IN +### v19.0.0 + +1) S13I and W152C positions added as critical because of https://science.sciencemag.org/content/early/2021/06/30/science.abi7994.full + + ### v18.0.0 1) S:K417N position added as critical because of https://www.reuters.com/business/healthcare-pharmaceuticals/what-is-delta-variant-coronavirus-with-k417n-mutation-2021-06-23/ diff --git a/cnr_curation_voc_qc.R b/cnr_curation_voc_qc.R index e557296e7794b660e99aba0ef753dfad79a4e7a9..6fc31a389b660f4bc3f72fa29abd1d5f69dd1abb 100644 --- a/cnr_curation_voc_qc.R +++ b/cnr_curation_voc_qc.R @@ -1023,7 +1023,7 @@ for(i0 in 1:nrow(res)){ # end tempo.qc positions converted to nextclade positions # coverage QC of all the voc variants using the .cov file - # cov file use the MN908947_Ampliseq positions + # cov file uses the MN908947_Ampliseq positions var.range <- paste0(tempo.qc$pos - dcov.ext, ":", tempo.qc$pos + dcov.ext) var.range.list <- lapply(as.list(var.range), FUN = function(x){eval(parse(text = x))}) range.cov <- lapply(var.range.list, FUN = function(x){cov[x, 3]}) diff --git a/dataset/20210626_critical_pos.txt b/dataset/20210704_critical_pos.txt similarity index 88% rename from dataset/20210626_critical_pos.txt rename to dataset/20210704_critical_pos.txt index 96053f2e793e7660c73529f392aed8fe0c99e9a5..c402a32bb2e320a2893d45aa6ca4d35ad97bbd85 100644 --- a/dataset/20210626_critical_pos.txt +++ b/dataset/20210704_critical_pos.txt @@ -1,6 +1,8 @@ # GATK positions for the deletions chr begin_pos end_pos codon_ref orf name ini_concern_name +MN908947_Ampliseq 21545 21547 AGT S S:S13 S:S13I MN908947_Ampliseq 21563 21565 ACA S S:T19 S:T19R +MN908947_Ampliseq 21962 21964 TGG S S:W152 S:W152C MN908947_Ampliseq 22757 22759 AAG S S:K417 S:K417N MN908947_Ampliseq 22826 22828 AAT S S:N440 S:N440K MN908947_Ampliseq 22862 22864 CTG S S:L452 S:L452R