Software and Hardware requirements

  • For exome analysis of a 30,000 variant sample 4GB RAM should suffice.
  • For genome analysis of a 4,400,000 variant sample 12GB RAM should suffice.
  • Any 64-bit operating system
  • Java 8 or above
  • At least 50GB free disk space (SSD preferred for best performance)
  • An internet connection is not required to run the Exomiser, although network access will be required if accessing a networked database (optional).
  • By default the Exomiser is completely self-contained and is able to run on standard consumer laptops.

Once the software has been installed according to the instructions, the exomiser can be run in a number of ways.

Exomiser

The original exomiser algorithm is easily run using the command-line arguments. Here we are using exomiser to prioritise variants from an exome containing a spiked in causative mutation for Pfeiffer syndrome:

10      123256215       .       T       G       100     PASS    GENE=FGFR2;INHERITANCE=AD;MIM=101600    GT:DS:GL        1|0:2.000:-5.00,-1.10,-0.04

The input parameters tell exomiser to read in in the VCF file (-v data/Pfeiffer.vcf) filter out variants using a frequency cuf-off of 1% (-F 1) and apply an autosomal dominant inheritance mode filter (-I AD). The patient phenotypes are described using the --hpo-ids argument and the exomiser is instructed to use the similarity matching algorithm containd in the hiPhive prioritiser --prioritiser hiphive. Other prioritisers can be specified as described in the prioritisers section.

java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --prioritiser hiphive -I AD -F 1 --hpo-ids HP:0000006,HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,HP:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304 -v data/Pfeiffer.vcf

Genomiser

The Genomiser uses the Exomiser framework to be able to analyse whole-genome data and has been especially tailored to include non-coding variants. It uses a config yml file instead of command-line arguments. To run your own samples you have to edit the test-analysis-genome.yml file and define

  • the location of your VCF,
  • the location of your PED-file (only for multiple samples in one VCF),
  • your patient’s HPO terms (use the HPO-Browser to find terms)
  • the inheritance model if known,
  • the outputPrefix for your output files.

We suggest all other options are left in their current state for optimal performance and until you have viewed the README.md file. Then run

java -Xms4g -Xmx8g -jar exomiser-cli-7.2.3.jar --analysis test-analysis-genome.yml

An example analysis containing a 5’ UTR variant can be run using this command:

java -Xms4g -Xmx8g -jar exomiser-cli-7.2.3.jar --analysis NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml

The NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml file is an exomiser analysis file for an autosomal recessive 5’UTR variant located in POMP gene on chromosome 13. The phenotype HPO terms are taken from the clinical synopsis of OMIM #601952

Prioritisers

The exomiser contains several different phenotype similarity algorithms specified using the --prioritiser argument. The sections below briefly describe the prioritisers and any special parameters they may require. The algorithms are described in detail in their respective publication.

hiPHIVE

Phenotype comparisons to human, mouse and fish involving disruption of the gene or nearby genes in the interactome using a RandomWalk:

Using an OMIM disease:

java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --prioritiser=hiphive -I AD -F 1 -D OMIM:101600 -v data/Pfeiffer.vcf

The same command using HPO-Terms (recommended):

java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --prioritiser=hiphive -I AD -F 1 --hpo-ids HP:0000006,HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,HP:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304 -v data/Pfeiffer.vcf

PHIVE

Phenotype comparisons to mice with disruption of the gene:

java -Xmx2g -jar exomiser-cli-7.2.3.jar --prioritiser=phive -I AD -F 1 -D OMIM:101600 -v data/Pfeiffer.vcf

Phenix

Phenotype comparisons to known human disease genes:

java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --prioritiser=phenix -v data/Pfeiffer.vcf -I AD -F 1 --hpo-ids HP:0000006,HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,HP:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304

ExomeWalker

Prioritisation by proximity in interactome to the seed genes:

java -Xms2g -Xmx4g -jar exomiser-cli-7.2.3.jar --prioritiser exomewalker  -v data/Pfeiffer.vcf -I AD -F 1 -S 2260