From ad0b0f3c8cb8244dec9509c413b894918f82940a Mon Sep 17 00:00:00 2001 From: Xiao Chen Date: Tue, 5 Dec 2023 14:55:06 -0800 Subject: [PATCH] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 92e72c7..889612d 100644 --- a/README.md +++ b/README.md @@ -73,7 +73,7 @@ Required parameters: - `-o`: Output directory - `-r`: Path to the reference genome fasta file -Please note that the input BAM should be one that's aligned to the ENTIRE reference genome (either GRCh38 or GRCh37/hg19), and this reference should NOT include ALT contigs. The fasta file of this reference genome should be provided to Paraphase with `-r`. +Please note that the input BAM should be one that's aligned to the ENTIRE reference genome (either GRCh38 or GRCh37/hg19), and this reference should NOT include ALT contigs. The fasta file of this reference genome should be provided to Paraphase with `-r`. Recommendations on reference genomes to use are documented [here](https://github.com/PacificBiosciences/reference_genomes). Optional parameters: - `-g`: Region(s) to analyze, separated by comma. All supported [regions](docs/regions.md) will be analyzed if not specified. Please use region name, i.e. first column in the doc.