From afc26e630d42ec47a171cd6522e5caae8108bb14 Mon Sep 17 00:00:00 2001 From: Jacek Marzec Date: Sun, 14 Jan 2024 22:21:02 +0000 Subject: [PATCH] Update link to PCGR tier documentation --- workflow.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflow.md b/workflow.md index 1e367121..d4f6ae61 100644 --- a/workflow.md +++ b/workflow.md @@ -153,8 +153,8 @@ For patients with available [WGS](./README.md#wgs) data processed using *[umccri ### Somatic SNVs and small indels * Check if **[PCGR](https://github.com/sigven/pcgr)** output file (see [example](./data/test_data/umccrised/test_sample_WGS/pcgr/test_sample_WGS-somatic.pcgr.snvs_indels.tiers.tsv)) is available -* **Extract** expression level **information** and genome-based findings for genes with detected genomic variants (use ```--pcgr_tier``` [argument](README.md/#arguments) to define [tier](https://pcgr.readthedocs.io/en/latest/tier_systems.html#tier-model-2-pcgr-acmg) threshold value) -* **Ordered genes** by increasing variants **[tier](https://pcgr.readthedocs.io/en/latest/tier_systems.html#tier-model-2-pcgr-acmg)** and then by decreasing absolute values representing difference between expression levels in the patient sample and the corresponding reference cohort +* **Extract** expression level **information** and genome-based findings for genes with detected genomic variants (use ```--pcgr_tier``` [argument](README.md/#arguments) to define [tier]([https://pcgr.readthedocs.io/en/latest/tier_systems.html#tier-model-2-pcgr-acmg](https://sigven.github.io/pcgr/articles/variant_classification.html) threshold value) +* **Ordered genes** by increasing variants **[tier]([https://pcgr.readthedocs.io/en/latest/tier_systems.html#tier-model-2-pcgr-acmg](https://sigven.github.io/pcgr/articles/variant_classification.html)** and then by decreasing absolute values representing difference between expression levels in the patient sample and the corresponding reference cohort ### Structural variants