From 5552fe0a9b7efe225e8cb9d79f0a9844dca742a5 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Tue, 7 May 2024 09:39:37 -0400 Subject: [PATCH] docs: update readme --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a0128e6..7858e81 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # LOGAN 🔬 [![Docker Pulls](https://img.shields.io/docker/pulls/nciccbr/ccbr_wes_base)](https://hub.docker.com/r/nciccbr/ccbr_wes_base) [![GitHub issues](https://img.shields.io/github/issues/ccbr/LOGAN?color=brightgreen)](https://github.com/ccbr/LOGAN/issues) [![GitHub license](https://img.shields.io/github/license/ccbr/LOGAN)](https://github.com/ccbr/LOGAN/blob/master/LICENSE) -> **_LOGAN-whoLe genOme-sequencinG Analysis pipeliNe_**. This is the home of the LOGAN Pipeline. Accurately call germline and somatic variants, CNVs, and SVs and annotate variants! +> **_LOGAN-whoLe genOme-sequencinG Analysis pipeliNe_**. Call germline and somatic variants, CNVs, and SVs and annotate variants! ## Overview Welcome to LOGAN! Before getting started, we highly recommend reading through [LOGAN's documentation](https://ccbr.github.io/LOGAN). @@ -72,7 +72,10 @@ Adding flags determines SNV (germline and/or somatic), SV, and/or CNV calling mo `--vc`- Enables somatic CNV calling using FREEC, Sequenza, and Purple (hg38 only) +#### Optional Arguments +`--indelrealign` - Enables indel realignment when running alignment steps. May be helpful for certain callers (VarScan, VarDict) +`--callers`- Comma separated argument for callers, the default is to use all available. Example: `--callers mutect2,octopus,vardict,varscan` ## Running LOGAN Example of Tumor only calling mode @@ -87,7 +90,7 @@ logan run --mode local -profile ci_stub --genome hg38 --outdir out --fastq_input logan run --mode slurm -profile biowulf,slurm --genome hg38 --outdir out --fastq_input "*R{1,2}.fastq.gz" --vc --sv --cnv ``` -We currently support the hg38 and mm10 genomes. +We currently support the hg38, hg19 (in progress), and mm10 genomes.