Sample MendelVar input:
User input is a tab-separated (.tsv), comma-separated (.csv) or space-separated table of single 1-indexed positions Accepted chromosome names: 1-22, X, Y. Accepted assemblies: GRCh37 (hg19) or GRCh38 (hg38).
Table needs to be header-less.
We accept two columns with chromosome and position. Examples:
chr1 10177
Or
1 10177
We also accept (and encourage) a third column with unique custom IDs, e.g.:
1 10177 rs367896724
If no custom ID is provided in the input, custom ID is created by MendelVar by concatenating the input chromosome and position, e.g. chr1_10177.
<aside> 💡 If you only have a list of SNP rsIDs and require to obtain their GRCh37 or GRCh38 genomic coordinates to run MendelVar, you can easily do so on the web using Ensembl Biomart GRCh37 or Ensembl Biomart GRCh38. An easy tutorial on how to do it available from 1000 Genomes.
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Going with the route 2 of input of single genomic positions, we need to first be able to generate genomic intervals which will be subsequently searched for overlap with Mendelian disease-causing genes and variants.
In route 2, user-specified left and right flank can be generated around the input positions, up to maximum of 10 Mbp in each direction to create custom fixed intervals.
MendelVar webserver accepts a maximum input of 10,000 intervals. Maximum size of every interval provided by user cannot exceed 20 Mbp.
Please contact the authors at [email protected] or [email protected], if you want to run a bigger job.