An in silico automated pipeline to identify tumor specific neoantigens from whole genome and exome sequencing data
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README.md
README.md~

README.md

Updated on 19, Jul. 2018.

1. Preparation

-Download and Set netMHCpan4.0 (Required)

  1. Download netMHCpan4.0 from http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan.

  2. Download a script from https://github.com/hase62/Neoantimon/raw/master/lib/setNetMHCpan4.0.sh and run it as "./setNetMHCpan4.0.sh".

-Download and Set netMHCIIpan3.1 (Required)

  1. Download netMHCIIpan 3.1 from http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan.

  2. Download a script from https://github.com/hase62/Neoantimon/raw/master/lib/setNetMHCIIpan3.1.sh and run it as "./setNetMHCIIpan3.1.sh".

-Download refMrna Files (Required)

You have to get your corresponding version from GRCh38, hg38, GRCh37 or hg19.

GRCh38/hg38: Download refMrna Files from "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/refMrna.fa.gz". Otherwise, run the following codes or use "InstallRefMrnaFile(url = "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/refMrna.fa.gz")" after installing Neoantimon.

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/refMrna.fa.gz
gunzip refMrna.fa.gz

GRCh37/hg19: Download refMrna Files from "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/refMrna.fa.gz". Otherwise, run the following codes or use "InstallRefMrnaFile(url = "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/refMrna.fa.gz")" after installing Neoantimon.

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/refMrna.fa.gz
gunzip refMrna.fa.gz

-Download refFlat Files (Required)

You have to get your corresponding version from GRCh38, hg38, GRCh37 or hg19.

GRCh38/hg38: Download refFlat Files from "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz". Otherwise, run the following codes or use "InstallRefFlat(url = "http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz")" after installing Neoantimon.

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz
gunzip refFlat.txt.gz

GRCh37/hg19: Download refFlat Files from "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz". Otherwise, run the following codes or use "InstallRefFlat(url = "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz")" after installing Neoantimon.

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
gunzip refFlat.txt.gz

-Install Samtools 0_x_x

Required for SV fusions. Not Required for Snv/Indel, but please download if you want to calculate Allele Specific RNA Expression based on RNA bam.

You can install samtools_0_x_x version from https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2. Otherwise, run the following codes or use "InstallSamtools()" after installing Neoantimon.

wget https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2
tar jxf samtools-0.1.19.tar.bz2
cd samtools-0.1.19
make
cd ..

-Download human refSeq

Required for SV fusions. Not Required for Snv/Indel, but please download if you want to calculate Allele Specific RNA Expression using RNA bam.

You have to get your corresponding version from GRCh38, hg38, GRCh37 or hg19.

GRCh38: Download human refSeq by

wget ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
mv Homo_sapiens.GRCh38.dna.toplevel.fa.gz GRCh38.fa.gz
gunzip GRCh38.fa.gz
samtools faidx GRCh38.fa

hg38: Download human refSeq by:

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz
samtools faidx hg38.fa

GRCh37: Download human refSeq:

wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.toplevel.fa.gz
mv Homo_sapiens.GRCh37.75.dna.toplevel.fa.gz GRCh37.fa.gz
gunzip GRCh37.fa.gz
samtools faidx GRCh37.fa

-Download SampleFiles

You can get these from https://github.com/hase62/Neoantimon/raw/master/lib/data.zip. Otherwise, run the following codes or use "InstallSampleFiles()" after installing Neoantimon.

wget https://github.com/hase62/Neoantimon/raw/master/lib/data.zip
unzip data.zip

2. Use on R

install.packages("devtools");
library(devtools);
install_github('hase62/Neoantimon');
library(Neoantimon);

3. Data Format

-HLA Table

1. A HLA Class I table file must be according to the following format.

library(Neoantimon)
data("sample_hla_table_c1")
print(sample_hla_table_c1, row.names = FALSE)
##     Name      A1      A2      B1      B2      C1      C2
##   sample A*02:01 A*32:01 B*15:17 B*51:01 C*07:01 C*15:02
##  sample2 A*02:01 A*32:01 B*15:17 B*51:01 C*07:01 C*15:02
##  ...

2. A HLA Class II table file must be according to the following format.

data("sample_hla_table_c2")
print(sample_hla_table_c2, row.names = FALSE)
##	Name	DPA11	DPA12	DPB11	DPB12	DQA11	DQA12	DQB11	DQB12	DRB11	DRB12
##	sample	DPA1*01:03	DPA1*02:01	DPB1*02:01	DPB1*09:01	DQA1*01:02	DQA1*05:05	DQB1*03:01	DQB1*06:04	DRB1*11:04	DRB1*13:02
##	sample2	DPA1*01:03	DPA1*02:01	DPB1*02:01	DPB1*09:01	DQA1*01:02	DQA1*05:05	DQB1*03:01	DQB1*06:04	DRB1*11:04	DRB1*13:02
##  ...

-Annotated VCF file

An annotated VCF file is required for Snv/Indel.

It must include columns representing "Chromosome Number", "Mutation Start Position", "Mutation End Position", "Mutation Ref", "Mutation Alt", and "NM_ID (AAChange.refGene)". Annotations "Chr", "Start", "End", "Ref", "Alt", "AAChange.refGene", "Depth_tumor", and "Depth_normal" are automatically detected. Otherwise, you have to manually indicate columns.

data("sample_vcf")
print(sample_vcf, row.names = FALSE)
## Chr     Start       End Ref Alt Func.refGene Gene.refGene   GeneDetail.refGene ExonicFunc.refGene                              AAChange.refGene   cytoBand depth_tumor variantNum_tumor depth_normal
##   1  47399872  47399872   A   G       exonic      CYP4A11        nonsynonymous                SNV      CYP4A11:NM_000778:exon8:c.T1064C:p.L355P       1p33          64               28           49
##   1 116941338 116941338   T   C       exonic       ATP1A1           synonymous                SNV   ATP1A1:NM_001160234:exon16:c.T2127C:p.D709D     1p13.1         100               39          111
##   4  24556416  24556416   T   C       exonic        DHX15        nonsynonymous                SNV        DHX15:NM_001358:exon5:c.A1012G:p.T338A     4p15.2         143               47          151
##   4  70156404  70156404   -   T       exonic      UGT2B28           frameshift          insertion   UGT2B28:NM_053039:exon5:c.1186dupT:p.L395fs     4q13.2          43               15           41
##   6  75899298  75899298   T   -       exonic      COL12A1           frameshift           deletion    COL12A1:NM_004370:exon6:c.628delA:p.I210fs       6q13         122               38           73
##   9  89561162  89561162   C   T       exonic         GAS1        nonsynonymous                SNV          GAS1:NM_002048:exon1:c.G533A:p.R178H    9q21.33          20                5           26

-Annotated BND format VCF file

An annotated BND format VCF file is required for SV fusion.

It must include columns representing "Chromosome Number", "Mutation Start Position", "Mutation End Position", "Mutation Ref", "Mutation Alt", and "NM_ID (AAChange.refGene)" or "Gene Symbol (Gene.refGene)". Annotations "Chr", "Start", "End", "Ref", "Alt", "Depth_tumor", and "Depth_normal" are automatically detected. Otherwise, you have to manually indicate columns.

data("sample_sv_bnd")
print(sample_sv_bnd, row.names = FALSE)
## Chr     Start       End Ref            Alt Func.refGene Gene.refGene           mateID
##   1 115005805 115005805   C C]20:34827929]       exonic       TRIM33     SVMERGE137_1
##   1 204908711 204908711   A [2:172743385[A     intronic        NFASC      SVMERGE15_1
##   2  25870534  25870534   T  ]2:25965720]G     intronic         DTNB     SVMERGE116_1
##   2  25965720  25965720   T  T[2:25870536[       exonic        ASXL2     SVMERGE116_2
##   2 214794791 214794791   C C[2:214798169[       exonic       SPAG16       SVMERGE3_1
##   2 214798169 214798169   T ]2:214794791]T     intronic       SPAG16       SVMERGE3_2

-RNAseq file

An RNAseq file is not required, but you can attach "RNA expression" information by indicating "rnaexp_file" in main functions. If you also indicate "rnabam_file", variant allele frequencies and tumor specific RNA expressions are also attached in the results.

data("sample_rna_exp")
print(sample_rna_exp, row.names = FALSE)
##  gene_short_name		   ChromosomeNum:Start-Endlocus expression
##              7SK    HSCHR6_MHC_MCF:30910595-30910898 0.00000000
##              7SK    HSCHR6_MHC_QBL:30821624-30821927 0.00000000
##              7SK                 X:12632121-12632316 0.00000000
##             A1BG                19:58856543-58864865 0.19541613
##         A1BG-AS1                19:58859116-58866549 5.30484229
##             A1CF                10:52559168-52645435 4.78487242
##              A2M                  12:9220259-9268825 0.75619084
##          A2M-AS1                  12:9217772-9220651 4.15985770
##            A2ML1                  12:8975067-9039597 7.50201326
##        A2ML1-AS1                  12:8928814-8983543 0.00000000
##        A2ML1-AS2                  12:8972411-8973309 7.02685468
##            A2MP1                  12:9381128-9428413 4.36764217
##          A3GALT2                 1:33772366-33786699 0.00000000
##           A4GALT                22:43088126-43117304 2.27225123
##            A4GNT               3:137842559-137851229 0.00000000
##             AAAS                12:53701239-53718648 1.45197987
##             AACS              12:125549924-125627873 7.34085879
##           AACSP1               5:178191861-178245436 4.07342571
##            AADAC               3:151531824-151546276 0.61589770
##          AADACL2               3:151451703-151479127 0.01359431
##          AADACL2 HSCHR3_1_CTG2_1:151462241-151489665 0.00000000

-CNV file

A copynumber file is not required, but you can attach "Copy Number" information by indicating "cnv_file" and "purity" in main functions. They are used to calculate tumor subclonal cell population Purity is set 1 as default value.

data("sample_copynum")
print(sample_copynum, row.names = FALSE)
##	Chromosome	Position	     Log.R	segmented.LogR	BAF	segmented.BAF	Copy.number	Minor.allele	Raw.copy.number
##			 1	  564621	 0.6071447	 -0.09862298	  1			   NA			  2			   1		  4.3540752
##			 1	  799463	 0.1519967	 -0.09862298	  1			   NA			  2			   1		  2.1467339
##			 1	  1017216	 0.8146911	 -0.09862298	  0			   NA			  3			   1		  5.8658499
##			 1	  1158277	-1.9594627	 -0.09862298	  0			   NA			  1			   0		 -0.5035897
##			 1	  1242215	 0.2927962	 -0.09862298	  0			   NA			  2			   1		  2.6999875
##			 1	  1462766	-0.2234090	 -0.09862298	  1			   NA			  2			   1		  1.0726687

4. Sample Codes

Sample files can be downloaded from https://github.com/hase62/Neoantimon/raw/master/lib/data.zip.
lib/data/sample_result_INDEL_CLASS1_ALL.txt
lib/data/sample_result_INDEL_CLASS2_ALL.txt
lib/data/sample_result_SeqFragment_CLASS1_ALL.txt
lib/data/sample_result_SeqFragment_CLASS2_ALL.txt
lib/data/sample_result_SNV_CLASS1_ALL.txt
lib/data/sample_result_SNV_CLASS2_ALL.txt
lib/data/sample_result_SVFusion_CLASS1_ALL.txt
lib/data/sample_result_SVFusion_CLASS2_ALL.txt
lib/data/sample_copynum.txt
lib/data/sample_hla_table_c1.txt
lib/data/sample_hla_table_c2.txt
lib/data/sample_rna_exp.txt
lib/data/sample_vcf.txt
lib/data/sample_sv_bnd.txt
Prepare the following files using the above explanations.
lib/netMHCpan-4.0
lib/netMHCIIpan-3.1  
lib/samtools-0.1.19
lib/refFlat.txt 
lib/refMrna.fa
lib/GRCh37.fa
Preparation
install.packages("devtools");
library(devtools);
install_github('hase62/Neoantimon');
library(Neoantimon);
Calculate Neoantigens on SNVs/INDELs for HLA Class I and II.
  Result_HLA1_SNV <- MainSNVClass1(input_file = "lib/data/sample_vcf.txt",
                                   file_name_in_hla_table = "sample",
                                   hla_file = "lib/data/sample_hla_table_c1.txt",
                                   refflat_file  = "lib/refFlat.txt",
                                   refmrna_file = "lib/refMrna.fa",
                                   rnaexp_file = "lib/data/sample_rna_exp.txt",
                                   netMHCpan_dir = "lib/netMHCpan-4.0/netMHCpan",
                                   depth_tumor_column = 12,
                                   depth_normal_column = 14
  )

  Result_HLA2_SNV <- MainSNVClass2(input_file = "lib/data/sample_vcf.txt",
                                   file_name_in_hla_table = "sample",
                                   hla_file = "lib/data/sample_hla_table_c2.txt",
                                   refflat_file  = "lib/refFlat.txt",
                                   refmrna_file = "lib/refMrna.fa",
                                   rnaexp_file = "lib/data/sample_rna_exp.txt",
                                   netMHCIIpan_dir = "lib/netMHCIIpan-3.1/netMHCIIpan",
                                   depth_tumor_column = 12,
                                   depth_normal_column = 14
  )

  Result_HLA1_INDEL <- MainINDELClass1(input_file = "lib/data/sample_vcf.txt",
                                       file_name_in_hla_table = "sample",
                                       hla_file = "lib/data/sample_hla_table_c1.txt",
                                       refflat_file  = "lib/refFlat.txt",
                                       refmrna_file = "lib/refMrna.fa",
                                       rnaexp_file = "lib/data/sample_rna_exp.txt",
                                       netMHCpan_dir = "lib/netMHCpan-4.0/netMHCpan",
                                       depth_tumor_column = 12,
                                       depth_normal_column = 14
  )

  Result_HLA2_INDEL <- MainINDELClass2(input_file = "lib/data/sample_vcf.txt",
                                       file_name_in_hla_table = "sample",
                                       hla_file = "lib/data/sample_hla_table_c2.txt",
                                       refflat_file  = "lib/refFlat.txt",
                                       refmrna_file = "lib/refMrna.fa",
                                       rnaexp_file = "lib/data/sample_rna_exp.txt",
                                       netMHCIIpan_dir = "lib/netMHCIIpan-3.1/netMHCIIpan",
                                       depth_tumor_column = 12,
                                       depth_normal_column = 14
  )
Calculate Neoantigens on SV fusions for HLA Class I and II.
  Result_HLA1_SV <- MainSVFUSIONClass1(input_file = "lib/data/sample_sv_bnd.txt",
                                       file_name_in_hla_table = "sample",
                                       hla_file = "lib/data/sample_hla_table_c1.txt",
                                       refflat_file  = "lib/refFlat.txt",
                                       refmrna_file = "lib/refMrna.fa",
                                       rnaexp_file = "lib/data/sample_rna_exp.txt",
                                       netMHCpan_dir = "lib/netMHCpan-4.0/netMHCpan",
                                       refdna_file = "lib/GRCh37.fa",
                                       mutation_alt_bnd_column = 5,
                                       gene_symbol_column = 7,
                                       mate_id_column = 8
  )

  Result_HLA2_SV <- MainSVFUSIONClass2(input_file = "lib/data/sample_sv_bnd.txt",
                                       file_name_in_hla_table = "sample",
                                       hla_file = "lib/data/sample_hla_table_c2.txt",
                                       refflat_file  = "lib/refFlat.txt",
                                       refmrna_file = "lib/refMrna.fa",
                                       rnaexp_file = "lib/data/sample_rna_exp.txt",
                                       netMHCIIpan_dir = "lib/netMHCIIpan-3.1/netMHCIIpan",
                                       refdna_file = "lib/GRCh37.fa",
                                       mutation_alt_bnd_column = 5,
                                       gene_symbol_column = 7,
                                       mate_id_column = 8
  )
Calculate Neoantigens from a fragment of RNA sequence for HLA Class I and II by comparing to the original protein.
  Result_HLA1_Seq <- MainSeqFragmentClass1(input_sequence = c("atggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc",
  															  "tggcagaagatgatccatatttgggaaggcctgaaaaaatgtttcatttggatccttctttgactcatacaatatttaatc"),
                                           file_name_in_hla_table = "sample",
                                           hla_file = "lib/data/sample_hla_table_c1.txt",
                                           hmdir = getwd(),
                                           job_id = "NO_job_id",
                                           refflat_file  = "lib/refFlat.txt",
                                           refmrna_file = "lib/refMrna.fa",
                                           netMHCpan_dir = "lib/netMHCpan-4.0/netMHCpan",
                                           nm_id = c("NM_003998", "NM_001165412"),
                                           reading_frame = 1
  )

  Result_HLA2_Seq <- MainSeqFragmentClass2(input_nm_id = c("NM_003998", "NM_001165412"),
                                           file_name_in_hla_table = "sample",
                                           hla_file = "lib/data/sample_hla_table_c2.txt",
                                           hmdir = getwd(),
                                           job_id = "NO_job_id",
                                           refflat_file  = "lib/refFlat.txt",
                                           refmrna_file = "lib/refMrna.fa",
                                           netMHCIIpan_dir = "lib/netMHCIIpan-3.1/netMHCIIpan",
                                           gene_symbol = c("NFKB1", "BCL3"),
                                           reading_frame = 3
  )

5. Result

They're also included in Result_HLA_*

sample_result_SNV_CLASS1_ALL.txt

##           HLA Pos    Gene Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank
## 1 HLA-A*02:01   2 0_DHX15            EPERDYLEAAIRA  37952.9  63.3899
## 2 HLA-A*02:01   3 0_DHX15            PERDYLEAAIRAV  12108.2  16.5100
## 3 HLA-A*02:01   4 0_DHX15            ERDYLEAAIRAVI  12109.5  16.5114
## 4 HLA-A*02:01   5 0_DHX15            RDYLEAAIRAVIQ  32063.2  46.0009
## 5 HLA-A*02:01   6 0_DHX15            DYLEAAIRAVIQI   4819.6   9.2763
## 6 HLA-A*02:01   7 0_DHX15            YLEAAIRAVIQIH   7309.7  11.8086
##   Evaluated_Wt_Peptide Wt_IC50 Wt_Rank Chr     NM_ID   Change Ref Alt Prob
## 1        EPERDYLEAAIRT 41213.3 75.7538   4 NM_001358 c.A1012G   T   C    0
## 2        PERDYLEAAIRTV 11859.7 16.2523   4 NM_001358 c.A1012G   T   C    0
## 3        ERDYLEAAIRTVI 14831.9 19.2905   4 NM_001358 c.A1012G   T   C    0
## 4        RDYLEAAIRTVIQ 33185.2 48.8110   4 NM_001358 c.A1012G   T   C    0
## 5        DYLEAAIRTVIQI  4504.5  8.9225   4 NM_001358 c.A1012G   T   C    0
## 6        YLEAAIRTVIQIH  6924.0 11.4357   4 NM_001358 c.A1012G   T   C    0
##   Mutation_Prob. Exon_Start Exon_End Mutation_Position Total_Depth
## 1              0   24529087 24586184        4_24556416         294
## 2              0   24529087 24586184        4_24556416         294
## 3              0   24529087 24586184        4_24556416         294
## 4              0   24529087 24586184        4_24556416         294
## 5              0   24529087 24586184        4_24556416         294
## 6              0   24529087 24586184        4_24556416         294
##   Tumor_Depth                  Wt_Peptide              Mutant_Peptide
## 1         143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD
## 2         143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD
## 3         143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD
## 4         143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD
## 5         143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD
## 6         143 PEPERDYLEAAIRTVIQIHMCEEEEGD PEPERDYLEAAIRAVIQIHMCEEEEGD
##   Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio
## 1   1.35204              NA        NA              0.6576249       NA
## 2   1.35204              NA        NA              0.6576249       NA
## 3   1.35204              NA        NA              0.6576249       NA
## 4   1.35204              NA        NA              0.6576249       NA
## 5   1.35204              NA        NA              0.6576249       NA
## 6   1.35204              NA        NA              0.6576249       NA
##   MutRatio_Min MutRatio_Max
## 1           NA           NA
## 2           NA           NA
## 3           NA           NA
## 4           NA           NA
## 5           NA           NA
## 6           NA           NA

sample_result_INDEL_CLASS1_ALL.txt

##           HLA Pos      Gene Evaluated_Mutant_Peptide_Core
## 1 HLA-A*02:01   1 0_UGT2B28                    GIPMVGIPLV
## 2 HLA-A*02:01   2 0_UGT2B28                 YHGIPMVGIPLVL
## 3 HLA-A*02:01   3 0_UGT2B28                  HGIPMVGIPLVL
## 4 HLA-A*02:01   4 0_UGT2B28                    GIPMVGIPLV
## 5 HLA-A*02:01   5 0_UGT2B28                    IPMVGIPLVL
## 6 HLA-A*02:01   2 0_UGT2B28                    GIPMVGIPLV
##   Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr     NM_ID         Change
## 1            IYHGIPMVGIPLV   8158.7  12.6683   4 NM_053039 Out_c.1186dupT
## 2            YHGIPMVGIPLVL    264.7   1.9668   4 NM_053039 Out_c.1186dupT
## 3            HGIPMVGIPLVLG  14185.4  18.6104   4 NM_053039 Out_c.1186dupT
## 4            GIPMVGIPLVLGS  13299.6  17.6940   4 NM_053039 Out_c.1186dupT
## 5            IPMVGIPLVLGST  17674.7  22.4056   4 NM_053039 Out_c.1186dupT
## 6             YHGIPMVGIPLV   5439.5   9.9316   4 NM_053039 Out_c.1186dupT
##   Ref Alt Prob Mutation_Prob. Exon_Start Exon_End Mutation_Position
## 1   -   T    0              0   70146216 70160768        4_70156404
## 2   -   T    0              0   70146216 70160768        4_70156404
## 3   -   T    0              0   70146216 70160768        4_70156404
## 4   -   T    0              0   70146216 70160768        4_70156404
## 5   -   T    0              0   70146216 70160768        4_70156404
## 6   -   T    0              0   70146216 70160768        4_70156404
##   Total_Depth Tumor_Depth                   Wt_Peptide     Mutant_Peptide
## 1          84          43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX
## 2          84          43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX
## 3          84          43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX
## 4          84          43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX
## 5          84          43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX
## 6          84          43 IYHGIPMVGIPLFWDQPDNIAHMKAKGA IYHGIPMVGIPLVLGSTX
##   Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio
## 1         0              NA        NA                      0       NA
## 2         0              NA        NA                      0       NA
## 3         0              NA        NA                      0       NA
## 4         0              NA        NA                      0       NA
## 5         0              NA        NA                      0       NA
## 6         0              NA        NA                      0       NA
##   MutRatio_Min MutRatio_Max
## 1           NA           NA
## 2           NA           NA
## 3           NA           NA
## 4           NA           NA
## 5           NA           NA
## 6           NA           NA

sample_result_SVFusion_CLASS1_ALL.txt

##           HLA Pos       Gene Evaluated_Mutant_Peptide_Core
## 1 HLA-A*02:01   1 0_SLC25A12                 GDPHELRNIFLQL
## 2 HLA-A*02:01   2 0_SLC25A12                  DPHELRNIFLQL
## 3 HLA-A*02:01   3 0_SLC25A12                   ELRNIFLQLSA
## 4 HLA-A*02:01   4 0_SLC25A12                 HELRNIFLQLSAV
## 5 HLA-A*02:01   5 0_SLC25A12                  ELRNIFLQLSAV
## 6 HLA-A*02:01   6 0_SLC25A12                   LRNIFLQLSAV
##   Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank Chr               NM_ID
## 1            GDPHELRNIFLQL   7994.3  12.5026   2 NM_003705_NM_015090
## 2            DPHELRNIFLQLS  36655.0  59.0000   2 NM_003705_NM_015090
## 3            PHELRNIFLQLSA  31164.0  43.8594   2 NM_003705_NM_015090
## 4            HELRNIFLQLSAV   2243.7   6.1823   2 NM_003705_NM_015090
## 5            ELRNIFLQLSAVQ  20527.4  25.8717   2 NM_003705_NM_015090
## 6            LRNIFLQLSAVQE  22787.8  28.8756   2 NM_003705_NM_015090
##                            Change Ref            Alt Prob Mutation_Prob.
## 1 In_SLC25A12_intron_NFASC_intron   A [1:204908711[A    0              0
## 2 In_SLC25A12_intron_NFASC_intron   A [1:204908711[A    0              0
## 3 In_SLC25A12_intron_NFASC_intron   A [1:204908711[A    0              0
## 4 In_SLC25A12_intron_NFASC_intron   A [1:204908711[A    0              0
## 5 In_SLC25A12_intron_NFASC_intron   A [1:204908711[A    0              0
## 6 In_SLC25A12_intron_NFASC_intron   A [1:204908711[A    0              0
##   Exon_Start  Exon_End Mutation_Position Total_Depth Tumor_Depth
## 1  172639914 172750816       2_172743385           0           0
## 2  172639914 172750816       2_172743385           0           0
## 3  172639914 172750816       2_172743385           0           0
## 4  172639914 172750816       2_172743385           0           0
## 5  172639914 172750816       2_172743385           0           0
## 6  172639914 172750816       2_172743385           0           0
##   Wt_Peptide
## 1 MAVKVQTT...
## 2 MAVKVQTT...
## 3 MAVKVQTT...
## 4 MAVKVQTT...
## 5 MAVKVQTT...
## 6 MAVKVQTT...
##                                                      Mutant_Peptide
## 1 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG
## 2 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG
## 3 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG
## 4 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG
## 5 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG
## 6 GDPHELRNIFLQLSAVQEAQLKRLEVTRPRVLGSREQGQVPRMARQPPPPWVHAAFLLCLLSLGG
##   Total_RNA Tumor_RNA_Ratio Tumor_RNA Tumor_RNA_based_on_DNA MutRatio
## 1   5.24517              NA        NA                    NaN       NA
## 2   5.24517              NA        NA                    NaN       NA
## 3   5.24517              NA        NA                    NaN       NA
## 4   5.24517              NA        NA                    NaN       NA
## 5   5.24517              NA        NA                    NaN       NA
## 6   5.24517              NA        NA                    NaN       NA
##   MutRatio_Min MutRatio_Max
## 1           NA           NA
## 2           NA           NA
## 3           NA           NA
## 4           NA           NA
## 5           NA           NA
## 6           NA           NA

sample_result_SeqFragment_CLASS1_ALL.txt

##           HLA Pos    Gene Evaluated_Mutant_Peptide_Core
## 1 HLA-A*02:01   1 0_NFKB1                 MAEDDPYLGRPEK
## 2 HLA-A*02:01   2 0_NFKB1                 AEDDPYLGRPEKM
## 3 HLA-A*02:01   3 0_NFKB1                     YLGRPEKMF
## 4 HLA-A*02:01   4 0_NFKB1                    YLGRPEKMFH
## 5 HLA-A*02:01   5 0_NFKB1                   YLGRPEKMFHL
## 6 HLA-A*02:01   6 0_NFKB1                   YLGRPEKMFHL
##   Evaluated_Mutant_Peptide Mut_IC50 Mut_Rank       Chr
## 1            MAEDDPYLGRPEK  34529.5  52.6059 chr4;chr4
## 2            AEDDPYLGRPEKM  37395.3  61.4560 chr4;chr4
## 3            EDDPYLGRPEKMF  41328.0  76.2274 chr4;chr4
## 4            DDPYLGRPEKMFH  42864.6  82.5363 chr4;chr4
## 5            DPYLGRPEKMFHL   3345.9   7.5921 chr4;chr4
## 6            PYLGRPEKMFHLD  19715.7  24.8190 chr4;chr4
##                    NM_ID      Change Ref Alt Prob Mutation_Prob.
## 1 NM_003998;NM_001165412 NFKB1;NFKB1  NA  NA   NA             NA
## 2 NM_003998;NM_001165412 NFKB1;NFKB1  NA  NA   NA             NA
## 3 NM_003998;NM_001165412 NFKB1;NFKB1  NA  NA   NA             NA
## 4 NM_003998;NM_001165412 NFKB1;NFKB1  NA  NA   NA             NA
## 5 NM_003998;NM_001165412 NFKB1;NFKB1  NA  NA   NA             NA
## 6 NM_003998;NM_001165412 NFKB1;NFKB1  NA  NA   NA             NA
##            Exon_Start            Exon_End Mutation_Position Total_Depth
## 1 103422485;103422485 103538459;103538459      chr4;chr4_NA          NA
## 2 103422485;103422485 103538459;103538459      chr4;chr4_NA          NA
## 3 103422485;103422485 103538459;103538459      chr4;chr4_NA          NA
## 4 103422485;103422485 103538459;103538459      chr4;chr4_NA          NA
## 5 103422485;103422485 103538459;103538459      chr4;chr4_NA          NA
## 6 103422485;103422485 103538459;103538459      chr4;chr4_NA          NA
##   Tumor_Depth
## 1          NA
## 2          NA
## 3          NA
## 4          NA
## 5          NA
## 6          NA
##   Wt_Peptide
## 1 MAEDDPY...
## 2 MAEDDPY...
## 3 MAEDDPY...
## 4 MAEDDPY...
## 5 MAEDDPY...
## 6 MAEDDPY...
##              Mutant_Peptide Total_RNA Tumor_RNA_Ratio Tumor_RNA
## 1 MAEDDPYLGRPEKMFHLDPSLTHTI        NA              NA        NA
## 2 MAEDDPYLGRPEKMFHLDPSLTHTI        NA              NA        NA
## 3 MAEDDPYLGRPEKMFHLDPSLTHTI        NA              NA        NA
## 4 MAEDDPYLGRPEKMFHLDPSLTHTI        NA              NA        NA
## 5 MAEDDPYLGRPEKMFHLDPSLTHTI        NA              NA        NA
## 6 MAEDDPYLGRPEKMFHLDPSLTHTI        NA              NA        NA
##   Tumor_RNA_based_on_DNA MutRatio MutRatio_Min MutRatio_Max
## 1                     NA       NA           NA           NA
## 2                     NA       NA           NA           NA
## 3                     NA       NA           NA           NA
## 4                     NA       NA           NA           NA
## 5                     NA       NA           NA           NA
## 6                     NA       NA           NA           NA