Inputs

inputs

Input Details

ID Label Type Required Format
input_bam input_bam File Yes BAM
input_reference_file input_reference_file File Yes TAR.GZ
input_file input_file File Yes VCF TXT
input_database_file input_database_file File Yes FASTA
input_allele_database input_allele_database File Yes fasta
input_gtf input_gtf_1 File Yes GTF
input_csv input_csv_1 File Yes CSV
input_bam
Input BAM file to call neoepitopes
input_reference_file
This is the Variant Effect Predictor reference file. This can be downloaded from the following link. homo_sapiens_vep_83_GRCh37.tar.gz
input_file
Input VCF file to call neoepitopes
input_database_file
This is the IMGT hla_prot.fasta file for input to netmhcpan. The input file must be formatted as below:
# The header in this file must be formated and renamed as netmhcpan-3.0.imgt.fasta
cat hla_prot.fasta |  perl -ne 'chomp;if(/\>\S+\s+(\S+)/){print ">$1\n";}else{print "$_\n";}' > netmhcpan-3.0.imgt.fasta
input_allele_database

This is the Hlaminer/IMGT database file, which can be downloaded from the following link: HLAminer Database. The index files can be obtained from the same link.

RNA-Seq data analysis
All files starting with HLA-I_II_CDS.* must be copied for RNA-seq analysis. The HLA-I_II_CDS.fasta comprises all IMGT/HLA HLA CDS (including class I and II).
DNA-Seq data analysis
All files starting with HLA-I_II_GEN.* must be copied for DNA-seq analysis. The HLA-I_II_GEN.fasta comprises all IMGT/HLA HLA genomic sequences (including class I and II).

Note

instructions to build the IMGT/HLA database are here on hlaminer github repository.

If you would like to update the coding sequences database(HLA-I_II_CDS.fasta), the instructions are provided here on the HLAminer github repository.

If you would like to update the genomics sequences database(HLA-I_II_GEN.fasta), the instructions are provided here on the HLAminer github repository.

input_gtf
Input Homo sapiens GTF file from Ensembl: Homo_sapiens.GRCh37.75.gtf.gz.
input_csv
Human Proteins (GRCh37.75) file: HumanProteins.GRCh37.75.csv.