From 83589751310902bbd1ccc030ccf505bd99f0e83c Mon Sep 17 00:00:00 2001 From: Sergey Senkin Date: Fri, 1 Dec 2023 15:57:07 +0100 Subject: [PATCH] Correcting README --- README.md | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c6fe168..7e1b5d0 100644 --- a/README.md +++ b/README.md @@ -43,11 +43,25 @@ Make sure you have the following dependencies installed before running the pipel ## Input -The directory with input VCF files specified by the `params.input_folder_with_VCF_files` parameter (by default, `./VCFs/*vcf.gz`) +| Name | Default value | Description | +|-----------|---------------|-----------------| +| `--output_foinput_folder_with_VCF_fileslder` | `${baseDir}/VCFs/` | Folder containing `*vcf.gz` files | + + +## Parameters + + * #### Optional + +| Name | Default value | Description | +|-----------|---------------|-----------------| +| `--reference_genome` | `GRCh37.75` | Folder containing `*vcf.gz` files | +| `--dbNSF_path` | `${baseDir}/dbNSFP4.1a.txt.gz` | [dbNSFP database](https://pcingola.github.io/SnpEff/ss_dbnsfp/) | +| `--dbSNP_path` | `${baseDir}/dbsnp150.vcf.gz` | [dbSNP database](https://ftp.ncbi.nlm.nih.gov/snp/organisms) | +| `--output_path` | `${baseDir}/output` | Output folder | ## Output -The final annotated and extracted information will be available in the `output` directory as `full_annotation.txt`. +The final annotated and extracted information will be available in the output directory as `full_annotation.txt`. ## Customization