config_VCF.yaml

##### Set path for input data 
# Output directory, it could be in absolute path (eg: /home/test)or relative path(eg: test/).
output_fold: VCF_test
# mutation file ,obtained from mutect2.
vcf_file: VCF_example_data/example_mutect2.vcf
sample_name: test
# Set hla allele for neoantigen identification, separated by comma and up to six hla types, eg:HLA-A02:01,HLA-A24:02,HLA-B44:02,HLA-B15:01,HLA-C05:01,HLA-C07:02
hla_str: HLA-A02:01
# Expression profile, obtained from Kallisto
expression_file: VCF_example_data/example_abundance.tsv
# copynumber profile, obtained from sequenza
copynumber_profile: VCF_example_data/example_seg_copynumber.txt
# tumor cellularity, also obtained from sequenza
tumor_cellularity: 0.33
# Set neoantigen peptide length, separatd by comma, eg: 9,10,11.
peptide_length: 9

##### Some filters parameter
#Minimal read depth for altenative allele
tumor_depth_cutoff: 10
#Minimal variant allele frequency for altenative allele
tumor_vaf_cutoff: 0.05
#Minimal variant allele frequency for reference allele
normal_vaf_cutoff: 0.03
# Fold change between MHC-mutant-peptide-binding-affinity and MHC-normal-peptide-binding-affinity, 1 means they are equal.
binding_fc_aff_cutoff: 1
# MHC-mutant-peptide binding affinity rank cutoff, usually set to 2.
binding_aff_cutoff: 2
# Expression value cutoff of neo-peptide, usually set to 1.
fpkm_cutoff: 0

##### specify other software excutable path in your system as you have installed them, make sure each tools could run.
vep_cache_path: your/path/to/vep_cache_data/
vep_path: your/path/to/vep
netMHCpan_path: your/path/to/netMHCpan
pyclone_path: your/path/to/PyClone