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How to annotate ClinVitae data from the sample VCF
GENE    Nucleotide change      protein change   ALIAS   Region
RASA1   NM_002890.1:c.296C>T   p.Ala99Val       -       Exon 1

This is how ClinVitae store the information, I need to find chromosome and positions(Start-stop) is there any way to find out?

vcf snp
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updated by Ram Ram • written by priyag8179 • priyag8179

2 answers

Using my tool backlocate:

BED interval: hg19: chr5:86564562-86564565 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr5%3A86564563-86564565

##uc003kiw.3
RASA1   A       99      V       uc003kiw.3      +       A     294     GCT     G       5       86564562        Exon 1
RASA1   A       99      V       uc003kiw.3      +       A     295     GCT     C       5       86564563        Exon 1
RASA1   A       99      V       uc003kiw.3      +       A     296     GCT     T       5       86564564        Exon 1
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Though it is difficult to read, you can use mutalyzer (PositionConverter) to convert the Nucleotide change into genomic coordinates.

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updated by Ram Ram • written by bioguy24 bioguy24

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