Customized protein database construction

Introduction

Customprodbj is a Java-based tool for customized protein database construction:

• Build a customized database based on single VCF file.
• Build a customized database based on multiple VCF files from a sample.
• Build a customized database based on multiple VCF files from multiple samples.

Usage

Please download Customprodbj program from the release page: https://github.com/bingzhang16/customprodbj/releases

java -jar customprodbj.jar

 -d      mRNA fasta database
 -f      A file which includes multiple samples. This parameter is used to
         build a customized database for
 -h      Help
 -i      Annovar annotation result file. Multiple files are separated by
         ','.
 -o      Output folder
 -p1     The prefix of variant protein ID, default is VAR_
 -p2     The prefix of final output files, default is merge
 -r      Gene annotation data
 -ref    Output reference protein database file
 -t      Whether or not to add reference protein sequences to the output
         database file
 -v      Verbose

Example

Build a customized database based on single VCF file

Step 1: Variant annotation using ANNOVAR:

perl table_annovar.pl test.vcf annovar_database/humandb/ -buildver hg19 -out out/test -protocol refGene -operation g -nastring . -vcfinput --thread 30 --maxgenethread 30 -polish

Step 2: Build customized protein database using Customprodbj:

java -jar customprodbj.jar -i test.hg19_multianno.txt -d annovar_database/humandb/hg19_refGeneMrna.fa -r annovar_database/humandb/hg19_refGene.txt -t -o out/

The input file "test.hg19_multianno.txt" is from ANNOVAR annotation result. The input files "annovar_database/humandb/hg19_refGeneMrna.fa" and "annovar_database/humandb/hg19_refGene.txt" are two files used by ANNOVAR. Before uses do variant annotation using ANNOVAR, users need to download these files using ANNOVAR. Please follow the instruction described here: http://annovar.openbioinformatics.org/en/latest/user-guide/download/.

Build a customized database based on multiple VCF files from a sample

Step 1: Variant annotation using ANNOVAR:

Perform variant annotation for each VCF file using the same method described in above section.

Step 2: Build customized protein database using Customprodbj:

java -jar customprodbj.jar -f input_variant_file_list.txt -d annovar_database/humandb/hg19_refGeneMrna.fa -r annovar_database/humandb/hg19_refGene.txt -t -o out/

The format of input_variant_file_list.txt looks like below:

sample  somatic germline    rna msi
sample1 s1a.hg19_multianno.txt  s1b.hg19_multianno.txt  s1c.hg19_multianno.txt  s1d.hg19_multianno.txt

Please note the columns are separated by "\t".

Build a customized database based on multiple VCF files from multiple samples

Step 1: Variant annotation using ANNOVAR:

Perform variant annotation for each VCF file using the same method described in above section.

Step 2: Build customized protein database using Customprodbj:

java -jar customprodbj.jar -f input_variant_file_list.txt -d annovar_database/humandb/hg19_refGeneMrna.fa -r annovar_database/humandb/hg19_refGene.txt -t -o out/

The format of input_variant_file_list.txt looks like below:

sample  somatic germline    rna msi
sample1 s1a.hg19_multianno.txt  s1b.hg19_multianno.txt  s1c.hg19_multianno.txt  s1d.hg19_multianno.txt
sample2 s2a.hg19_multianno.txt  s2b.hg19_multianno.txt  s2c.hg19_multianno.txt  s2d.hg19_multianno.txt
sample3 s3a.hg19_multianno.txt  s3b.hg19_multianno.txt  s3c.hg19_multianno.txt  s3d.hg19_multianno.txt

Ouput

The final outputs consist of three files:

*-varInfo.txt: A table contains the detailed amino acid change information. Each row is a variant.

*-var.fasta: Customized protein database.

*-varStat.txt: Summary data.

How to cite:

Wen, B., Li, K., Zhang, Y. et al. Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis. Nature Communications 11, 1759 (2020). https://doi.org/10.1038/s41467-020-15456-w