Frequently asked questions

How does Bystro handle missing data?

We won't impute missing numerical data ( null ) as 0

Ex: gnomad.exomes.af < .01 skips sites without reliable ( PASS ) gnomAD exomes data

To return missing sites use an OR query: gnomad.exomes.af < .01 || !gnomad.exomes

Can Bystro annotations be used for creating a Set ID for SKAT analyses?

Yes, here are some brief suggestions for generating your own Set ID:

• ▶
  Filter list on any terms of interest and save a new annotation from this query using the save button

  • ▶Ex: maf < .01, -intergenic, cadd > 15, lof
• ▶Cut out gnomad.genomes.id to get the variant names and refseq.name2 or refseq.nearest.name2 for the gene name.
• ▶Split the gene names and remove duplicates that occur from multiple transcripts
• ▶Replace sites that don't have an rs number with a value based on the chrom/pos
• ▶Use other columns such as gnomad.genomes.af or a specific population allele frequency for weighing SKAT analyses