A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.
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Correct HGVS nucleotide names to be indexed from the start of the reference genome #165
Currently, the HGVS nucleotide names from the VCFs, created by SnpEff, give the nucleotide mutation position as referenced from the start of the protein. HGVS recommendations require the position to be given with respect to the reference nucleotide sequence.
So, we can either:
1) rewrite those positions to match the number in the pos column, or
2) put the transcript identifier in brackets, eg. NG_012232.1(NM_004006.2):c.93G>T
Currently, the HGVS nucleotide names from the VCFs, created by SnpEff, give the nucleotide mutation position as referenced from the start of the protein. HGVS recommendations require the position to be given with respect to the reference nucleotide sequence.
So, we can either: 1) rewrite those positions to match the number in the
poscolumn, or 2) put the transcript identifier in brackets, eg.NG_012232.1(NM_004006.2):c.93G>T