Biowulf High Performance Computing at the NIH
SpliceAI: predicting splicing from primary sequence with deep learning

SpliceAI is a deep neural network that accurately predicts splice junctions from an arbitrary pre-mRNA transcript sequence, enabling precise prediction of noncoding genetic variants that cause cryptic splicing.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=8g --gres=gpu:v100:1
[user@cn4466 ~]$ module load SpliceAI
+] Loading python 3.6  ...
[+] Loading cuDNN 7.0  libraries...
[+] Loading CUDA Toolkit  9.0.176  ...
[user@cn4466 ~]$ spliceai -h
...
usage: spliceai [-h] [-I [input]] [-O [output]] -R reference -A annotation
                [-D [distance]] [-M [mask]]

Version: 1.3

optional arguments:
  -h, --help     show this help message and exit
  -I [input]     path to the input VCF file, defaults to standard in
  -O [output]    path to the output VCF file, defaults to standard out
  -R reference   path to the reference genome fasta file
  -A annotation  "grch37" (GENCODE V24lift37 canonical annotation file in
                 package), "grch38" (GENCODE V24 canonical annotation file in
                 package), or path to a similar custom gene annotation file
  -D [distance]  maximum distance between the variant and gained/lost splice
                 site, defaults to 50
  -M [mask]      mask scores representing annotated acceptor/donor gain and
                 unannotated acceptor/donor loss, defaults to 0
Download sample data:
[user@cn4466 ~]$ cp $SPLICEAI_DATA/* . 
Specify a reference sequence:
[user@cn4466 ~]$ ln -s  /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa hg38.fa
Run the spliceai executable on the sample data:
 
[user@cn4466 ~]$ spliceai -I input.vcf -O output.vcf -R hg38.fa  -A grch37
...
WARNING:root:Skipping record (ref issue): 2     152389953       .       T       A,C,G   .       .       .

WARNING:root:Skipping record (ref issue): 2     179415988       .       C       CA      .       .       .

WARNING:root:Skipping record (ref issue): 2     179446218       .       ATACT   A       .       .       .

WARNING:root:Skipping record (ref issue): 2     179446218       .       ATACT   AT,ATA  .       .       .

WARNING:root:Skipping record (ref issue): 2     179642185       .       G       A       .       .       .

WARNING:root:Skipping record (ref issue): 19    38958362        .       C       T       .       .       .

WARNING:root:Skipping record (ref issue): 21    47406854        .       CCA     C       .       .       .

WARNING:root:Skipping record (ref issue): 21    47406856        .       A       AT      .       .       .

WARNING:root:Skipping record (ref issue): X     129274636       .       A       C,G,T   .       .       .
An output file output.vcf will be produced:
[user@cn4466 ~]$ cat output.vcf
...
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       25000   .       A       C,G,T   .       .       .
2       152389953       .       T       A,C,G   .       .       .
2       179415988       .       C       CA      .       .       .
2       179446218       .       ATACT   A       .       .       .
2       179446218       .       ATACT   AT,ATA  .       .       .
2       179642185       .       G       A       .       .       .
19      38958362        .       C       T       .       .       .
21      47406854        .       CCA     C       .       .       .
21      47406856        .       A       AT      .       .       .
X       129274636       .       A       C,G,T   .       .       .
Exit the application:
[user@cn4466 ~]$ exit
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. spliceai.sh). For example:

#!/bin/bash
module load SpliceAI      
cp $SPLICEAI_DATA/* .  
spliceai -I input.vcf -O output.vcf -R /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa  -A grch37

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] spliceai.sh