From 707ad705cb11436e2d7588f7debabc4d663c5edb Mon Sep 17 00:00:00 2001 From: "Jaganathan, Kishore" Date: Wed, 14 Nov 2018 16:45:38 -0800 Subject: [PATCH] Update README.md --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index a182a4b..2ea6020 100644 --- a/README.md +++ b/README.md @@ -8,10 +8,6 @@ The simplest way to install SpliceAI is through pip: pip install spliceai ``` -SpliceAI requires [tensorflow](https://www.tensorflow.org/install/)>=1.2.0, -which is best installed separately via pip: `pip install tensorflow`. See -tensorflow website for complete installation options. - Alternately, SpliceAI can be installed from the [github repository](https://github.com/Illumina/SpliceAI.git): ```sh git clone https://github.com/Illumina/SpliceAI.git @@ -19,13 +15,17 @@ cd SpliceAI python setup.py install ``` +SpliceAI requires [tensorflow](https://www.tensorflow.org/install/)>=1.2.0, +which is best installed separately via pip: `pip install tensorflow`. See +the TensorFlow website for other installation options. + ### Usage SpliceAI can be run from the command line: ```sh spliceai -I input.vcf -O output.vcf -R genome.fa [-A annotations.tsv] # or you can pipe input and output VCFs -cat input.vcf | spliceai -R genome.fa > output.vcf +cat input.vcf | spliceai -R genome.fa [-A annotations.tsv] > output.vcf ``` Options: - **-I**: The input VCF with variants of interest. Only SNVs and simple indels @@ -41,7 +41,7 @@ Options: `spliceai/annotations/GENCODE.v24lift37` in repository as template for creating custom annotations). -Details of SpliceAI info field: +Details of SpliceAI INFO field: | ID | Description | | -------- | ----------- | @@ -58,7 +58,7 @@ Details of SpliceAI info field: **Delta score** of a variant ranges from 0 to 1, and can be interpreted as the probability of the variant being splice-altering. In the paper, a detailed characterization is provided for 0.2 (high recall/likely pathogenic), 0.5 (recommended/pathogenic), and 0.8 (high precision/pathogenic) cutoffs. **Delta position** conveys information about the location where splicing changes relative to the variant position (positive values are upstream of the variant, negative values are downstream). -For the sake of convenience, we have precomputed scores for all possible single nucleotide variants near genes, which are available [here](https://basespace.illumina.com/s/5u6ThOblecrh). +For the sake of convenience, we have precomputed scores for all possible single nucleotide variants within genes, which are available [here](https://basespace.illumina.com/s/5u6ThOblecrh). ### Examples A sample input file and the corresponding output file can be found at `examples/input.vcf` and `examples/output.vcf` respectively. The output `SpliceAI=T|RYR1|0.22|0.00|0.91|0.70|-107|-46|-2|90` for the variant `19:38958362 C>T` can be interpreted as follows: