Sigs

Fits sample SNV counts to trinucleotide signature definitions.

Configuration

To install, download the latest compiled jar file from the download links.

Resource Files

Sigs requires a signature definition file, for example the COSMIC 30 SNV signatures. These can be downloaded here HMFTools-Resources:

Mandatory Arguments

Argument	Description
sample	Sample ID
signatures_file	SNV signature definitions file
somatic_vcf_file	SNV VCF file
output_dir	Output directory for sample SNV fits

Optional Arguments

Argument	Default	Description
min_alloc	0.01	Allocate counts to a signature if exceeds this number of total SNV counts
min_alloc_perc	0.0005	Allocate counts to a signature if exceeds this % of total SNV counts
db_url,db_user,db_pass	-	My SQL config - for sourcing SNV data instead of from a VCF
upload_to_db	-	If present will upload signature fit results to the HMF Patients signature table

Position Frequency Arguments

Sigs can generate genomic position frequencies by rounding positions to a specified position bucket size.

Argument	Default	Description
position_bucket_size	0	0 means no position frequencies are generated, otherwise bucket size
max_sample_count	20000	Cap any individual position bucket's SNV count to this level

Example Usage

VCF sourced:

java -jar sigs.jar \
   -sample COLO829T 
   -signatures_file /reference_file/snv_cosmic_signatures.csv \
   -somatic_vcf_file /sample_data/COLO829T.purple.somatic.vcf.gz \
   -output_dir /output_dir/ \

Example Usage

Database sourced and uploading results

java -jar sigs.jar \
   -sample COLO829T 
   -signatures_file /reference_file/snv_cosmic_signatures.csv \
   -db_url [db_url] -db_user [username] -db_pass [password] \
   -upload_to_db \
   -output_dir /output_dir/ \