diff --git a/README.md b/README.md index b5653e2..cf96e8b 100644 --- a/README.md +++ b/README.md @@ -123,6 +123,15 @@ zcat [VCF after script] | grep -v '^#' | cut -f 10- | md5sum If the two checksums differ, it indicates that FORMAT fields were affected by the issue. +### Note: Recommended GIC Use Options + +For the [GIC](https://www.genomicinformationcommons.org) project, it's preferred to use the following options to ensure data consistencies across all participating institutions: + +* `--vep-gnomad-af gnomADg_AF` +* `--mode cds_rsid` + +Please don't use the `--pick` option. As of March 2025, the [PIC-SURE HPDS](https://github.com/hms-dbmi/pic-sure-hpds) genomic import process can now handle variants with multiple consequences and genes. This makes the `--pick` option no longer necessary for GIC portal purposes. + ### Python script options `-R `