Sample MendelVar input:
yap2018_baldness_grch38_interval.bed
User input is a tab-separated (.tsv), comma-separated (.csv) or space-separated table of user-provided genomic ranges in form of a 1-indexed closed (inclusive) interval (GFF3-style). Accepted chromosome names: 1-22, X, Y. Accepted assemblies: GRCh37 (hg19) or GRCh38 (hg38).
The table needs to be header-less.
We accept three columns with chromosome, start position, end position (inclusive). Examples:
chr1 9000 11000
Or
1 9000 11000
We also accept (and encourage) a fourth column with unique custom IDs, e.g.:
1 9000 11000 rs367896724
If no custom ID is provided in the input, custom ID is created by MendelVar by concatenating the input chromosome and positions, e.g. chr1_9000_11000.
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.
Overlap with genes is based on coordinates the CDS of canonical APPRIS transcript isoform for a given gene, if available, alternatively, the longest transcript for a given gene. Users can extend the gene region upstream and downstream by up to 20 kbp in each direction, if they want to increase the region of potential overlap with a test interval. Most of the strong eQTLs regulating gene expression are found in that region.
<aside> 💡 It is not recommended to extend 5 and 3' gene regions too much, as this can result in more genes overlapping each other and being collapsed into one ontology annotation by INRICH when calculating ontology term enrichment, which will then result in a loss of power in the gene INRICH mode.
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