SVS 8.7.1 Release Notes

New Features

  • The Genotype Imputation method has been updated to optionally utilize the Pedigree data provided by the input spreadsheet during phasing and imputation. This ensures more accurate haplotype matches for related samples and that output genotypes are free of Mendelian errors.
  • The phasing 4.1 algorithm has also had some optimizations applied to provide a modest performance improvement to the algorithm.
  • The PhoRank algorithm has been updated extensively to improve the ranking of genes relevant to sample phenotypes. Also, input phenotypes have been extended to include OMIM provided syndromes and phenotypes. The OMIM content add-on is required for this feature. (See PhoRank Gene Ranking for further details)
  • A number of updates and improvements have been made to the Annotate Variant Effect on Transcripts annotation algorithm that provides per-transcript variant interactions.
    • New fields in the Variant Interaction Report provide the reference and alternate Amino Acid for each transcript in the interactions table. Additionally the number of exons and amino acid position are provided.
    • The HGVS p. field was updated for synonymous and frameshift variants to be the long form. For synonymous variants, this includes the reference amino acid. For frameshift variants this includes the amino acid in the altered sequence.
    • Intronic variants now have their nearest exon reported in the Exon Number field, and a new field 5’ Exon Number can be used to determine which two exons the intronic variant is between.

Polishes

  • A number of updates have been made to the Genotype Imputation tool to improve usability.
    • Added in format checks to verify that spreadsheets contain marker mapped genotype data before the tools can be launched.
    • Allows the option to create reference panel as a spreadsheet for those users who want to fill in missing genotypes or correct genotyping errors in their target data.
    • When running imputation, an addition option allows all input markers to be passed through to the output, even when matching markers in the reference panel are not found.
  • Recode SNPs to Variants now allows the RSID to be specified by the column header and not just marker map fields.


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