Use external resources

use COSMIC

To use COSMIC with WGSA07 and later versions:

1. Create a folder named "COSMIC" under "resources". Create folders "hg19" and "hg38" under "COSMIC".

2. Obtain a copy of the GRCh37 and GRCh38 version of the CosmicCodingMuts.vcf.gz from COSMIC.

   • register an account at COSMIC using your email address

   • sftp "your_email_address"@sftp-cancer.sanger.ac.uk

   • sftp> get /cosmic/grch37/cosmic/v82/VCF/CosmicCodingMuts.vcf.gz

   • sftp> get /cosmic/grch38/cosmic/v82/VCF/CosmicCodingMuts.vcf.gz

3. Put the GRCh37 version CosmicCodingMuts.vcf.gz in the COSMIC/hg19 folder and the GRCh38 version in the COSMIC/hg38 folder.

4. In the configuration file, choose s(np), i(ndel) or b(oth) in the option line beginning with "COSMIC:".

use SPIDEX

To use SPIDEX free non-commercial version 1 of SPIDEX with WGSA055, WGSA06, WGSA065 and WGSA07:

1. Create a folder named "spidex" under resources.

2. Obtain a copy of the file spidex_public_noncommercial_v1_0.tab.gz from deep genomics.

3. Put the file spidex_public_noncommercial_v1_0.tab.gz in the spidex folder.

4. In the configuration file, choose s(np), i(ndel) or b(oth) in the option line beginning with "SPIDEX:".

To use the ANNOVAR version of SPIDEX with WGSA071 and later versions:

1. Create a folder named "spidex" under resources.

2. Obtain a copy of the file hg19_spidex.zip from the ANNOVAR website.

3. Unzip the file and put the file hg19_spidex.txt in the spidex folder.

4. In the configuration file, choose s(np), i(ndel) or b(oth) in the option line beginning with "SPIDEX:".

use CADD indel annotation

1. Run CADD v1.6 with your indel list (with or without additional annotations).

2. Rename (and gzip if not gzipped) the output file as CADD.out.gz and put the file in the work folder.

3. In the configuration file set the option of CADDindel as indel or i.

use dbNSFP4.0a (academic use only)

1. Download dbNSFP4.0a from softgenetics ftp or googledrive.

2. Unzip it to resources/dbNSFP/.

3. In the configuration file set the option of dbNSFPa_variant as snp or s.