Version 1.3

README.md

@@ -5,7 +5,7 @@
 
 This package annotates genetic variants with their predicted effect on splicing, as described in [Jaganathan *et al*, Cell 2019 in press](https://doi.org/10.1016/j.cell.2018.12.015).
 
-**Update**: SpliceAI annotations for all SNVs, 1-base insertions, and 1-4 base deletions within genes are available [here](https://basespace.illumina.com/s/5u6ThOblecrh) for download.
+**Update**: The annotations for all possible substitutions, 1 base insertions, and 1-4 base deletions within genes are available [here](https://basespace.illumina.com/analyses/194103939/files?projectId=66029966) for download.
 
 ### Installation
 The simplest way to install SpliceAI is through pip or conda:
@@ -34,8 +34,8 @@ cat input.vcf | spliceai -R genome.fa -A grch37 > output.vcf
 
 Required parameters:
  - ```-I```: Input VCF with variants of interest.
- - ```-O```: Output VCF with SpliceAI predictions `SpliceAI=ALLELE|SYMBOL|DS_AG|DS_AL|DS_DG|DS_DL|DP_AG|DP_AL|DP_DG|DP_DL` included in the INFO column (see table below for details). Only SNVs and simple INDELs (REF or ALT is a single base) within genes are annotated. Variants in multiple genes have separate predictions for each gene.
- - ```-R```: Reference genome fasta file ([GRCh37/hg19](http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz), [GRCh38/hg38](http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz)).
+ - ```-O```: Output VCF with SpliceAI predictions `ALLELE|SYMBOL|DS_AG|DS_AL|DS_DG|DS_DL|DP_AG|DP_AL|DP_DG|DP_DL` included in the INFO column (see table below for details). Only SNVs and simple INDELs (REF or ALT is a single base) within genes are annotated. Variants in multiple genes have separate predictions for each gene.
+ - ```-R```: Reference genome fasta file (for example: [GRCh37/hg19](http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz), [GRCh38/hg38](http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz)).
  - ```-A```: Gene annotation file. Can instead provide `grch37` or `grch38` to use GENCODE V24 canonical annotation files included with the package. To create custom gene annotation files, use `spliceai/annotations/grch37.txt` in repository as template.
 
 Optional parameters:
@@ -57,7 +57,7 @@ Details of SpliceAI INFO field:
 |  DP_DG   | Delta position (donor gain) |
 |  DP_DL   | Delta position (donor loss) |
 
-**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 downstream of the variant, negative values are upstream).
+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 downstream of the variant, negative values are upstream).
 
 ### Examples
 A sample input file and the corresponding output file can be found at `examples/input.vcf` and `examples/output.vcf` respectively (`grch37` annotation). The output `SpliceAI=T|RYR1|0.00|0.00|0.91|0.08|-28|-46|-2|-31` for the variant `19:38958362 C>T` can be interpreted as follows: