normalise and report

[PeterKnealeCMRI]

• move downloads
• Install validaotor
• Add normalise script
• Process both sources
• Use a single file
• Added report

[h-joshi]

Looks good. The c.-9+340= and c.518+118= are unusual in that there is no base change. i.e. c.-9+340= means that the nucleotide at position c.-9+340 is unchanged. I feel the CliinVar submitters have not checked this entry before submitting.

normalised_ensemble.vcf                                         normalised_variant_validator.vcf
chrX    63754408        NM_001353921.2:c.31-29709dup    a     <
chrX    124061743       NM_001042750.2:c.1535-15_1535-3del    <
                                                              > chrX    124061743       NM_001042750.2:c.1535-15_1535-3del
                                                              > chrX    154547128       NM_001042351.3:c.-9+340=        C
                                                              > chrX    154558768       NM_001099857.5:c.518+118=       G

Variant HGVS	Processed by Ensembl?	Processed by VariantValidator?	Processed by HGVS?	Similarity
NM_001353921.2:c.31-29709dup	Y	N	Y	Ensembl, HGVS
NM_001042750.2:c.1535-15_1535-3del	Y	Y	Y	Ensembl, VV, HGVS
NM_001042351.3:c.-9+340=	N	Y	N	N/A
NM_001099857.5:c.518+118=	N	Y	N	N/A