The current PSAP pipeline has been developed around ANNOVAR variant annotation. A few issues have arisen based on ANNOVAR conventions, and we are currently exploring the use of alternative variant annotation packages (e.g. VEP). There is a column of annotation beginning with "AAChange", containing a list of all possible amino acid change resulting from a variant, and a second column, "Gene.wgEncodeGencodeBasicV19", which provides a gene ID or list of gene IDs. in some cases, there is a mismatch between the geneIDs used in "AAChange" and the geneIDs listed in "Gene.wg...". Specifically, a geneID used in "AAChange" is missing from the geneIDs in "Gene.wg". This is problematic because we use the "Gene.wg.." column for determining which gene to use for PSAP lookup.
The current PSAP pipeline has been developed around ANNOVAR variant annotation. A few issues have arisen based on ANNOVAR conventions, and we are currently exploring the use of alternative variant annotation packages (e.g. VEP). There is a column of annotation beginning with "AAChange", containing a list of all possible amino acid change resulting from a variant, and a second column, "Gene.wgEncodeGencodeBasicV19", which provides a gene ID or list of gene IDs. in some cases, there is a mismatch between the geneIDs used in "AAChange" and the geneIDs listed in "Gene.wg...". Specifically, a geneID used in "AAChange" is missing from the geneIDs in "Gene.wg". This is problematic because we use the "Gene.wg.." column for determining which gene to use for PSAP lookup.