Added annotation files

README.md

@@ -16,7 +16,7 @@ A tool for simplifying snpEff annotations
 
 1. python 2.7
 2. [PyVcf](http://pyvcf.readthedocs.org/en/latest/) python module
-3. [VCF](https://vcftools.github.io/specs.html) file annotated with [snpEff v4.1g+](http://snpeff.sourceforge.net/).
+3. [VCF](https://vcftools.github.io/specs.html) file annotated with [snpEff v4.3+](http://snpeff.sourceforge.net/).
 
 ```simple_sv_annotation.py``` is designed around the new [ANN](http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf) annotation field rather than the previous EFF field.
 
@@ -37,7 +37,8 @@ vcf FILE - vcf file annotated with snpEff v4.1g+
 ```
 --output/-o   FILE - Output file name. Default: <invcf>.simpleann.vcf
 --exonNums/-e FILE - List of custom exon numbers (see Alternate Exon Numbers)
--r                 - Replace the ANN field instead of adding SIMPLE ANN (see Example Output)
+--gene_list/-g FILE - List of genes to prioritise on
+--known_fusion_pairs/-k FILE - Comma delimited file with a gene pair on each row representing known fusion pairs
 ```
 
 ## Alternate Exon Numbers
@@ -99,7 +100,7 @@ Jenkins, [AZ Email](mailto:david.jenkins1@astrazeneca.com) or [BU Email](mailto:
 1. Intergenic SVs
 2. Intronic SVs
 3. Whole Exon Loss SVs
-4. Gene Fusions Annotated as breakends
+4. Gene Fusions (can result from BND/DEL/INV/DUP)
 
 Examples of the simplified SV annotations are below.
 
@@ -149,20 +150,3 @@ after:
 
 chr17  41258467  del_5  ATATACCTTTTGGTTATATCATTCTTACATAAAGGACACTGTGAAGGCCCTTTCTTCTGGTTGAGAAGTTTCAGCATGCAAAATCTATA  A  .  .  END=41258555;SVTYPE=DEL;SVLEN=-88;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;ANN=A|exon_loss_variant&splice_acceptor_variant&splice_donor_variant&splice_region_variant&splice_region_variant&splice_region_variant&splice_region_variant&intron_variant&intron_variant|HIGH|BRCA1|BRCA1|transcript|NM_007294.3|Coding|4/23|c.135-5_212+5delTATAGATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGTATA||||||;SIMPLE_ANN=DEL|EXON_DEL|BRCA1|NM_007294.3|Exon5del
 ```
-
-#### 2. Replace ANN field 
-
-Optionally, you may choose to replace the 16 column ANN field with the simplified
-annotation information. This will roughly preserve the type of information
-expected in each field. The five fields of the SIMPLE_ANN annotation will be
-placed in the 1st, 2nd, 4th, 7th, and 9th column of the ANN record
-
-```
-before:
-
-chr17  41258467  del_5  ATATACCTTTTGGTTATATCATTCTTACATAAAGGACACTGTGAAGGCCCTTTCTTCTGGTTGAGAAGTTTCAGCATGCAAAATCTATA  A  .  .  END=41258555;SVTYPE=DEL;SVLEN=-88;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;ANN=A|exon_loss_variant&splice_acceptor_variant&splice_donor_variant&splice_region_variant&splice_region_variant&splice_region_variant&splice_region_variant&intron_variant&intron_variant|HIGH|BRCA1|BRCA1|transcript|NM_007294.3|Coding|4/23|c.135-5_212+5delTATAGATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGTATA||||||
-
-after:
-
-chr17  41258467  del_5  ATATACCTTTTGGTTATATCATTCTTACATAAAGGACACTGTGAAGGCCCTTTCTTCTGGTTGAGAAGTTTCAGCATGCAAAATCTATA  A  .  .  END=41258555;SVTYPE=DEL;SVLEN=-88;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0;ANN=DEL|EXON_DEL||BRCA1|||NM_007294.3||Exon5del|||||||
-```

az-cancer-panel.txt

@@ -0,0 +1,316 @@
+RPL22
+ERRFI1
+PIK3CD
+MTOR
+ARID1A
+MYCL
+MPL
+MUTYH
+CDKN2C
+PRKAA2
+JAK1
+RPL5
+NRAS
+NOTCH2
+BCL9
+MCL1
+RIT1
+NTRK1
+B4GALT3
+DDR2
+ELF3
+PIK3C2B
+MDM4
+AKT3
+MYCN
+DNMT3A
+ALK
+SOS1
+MSH2
+MSH6
+PCBP1
+INPP4A
+ACVR2A
+NFE2L2
+PMS1
+SF3B1
+IDH1
+ERBB4
+VHL
+RAF1
+TGFBR2
+MLH1
+CTNNB1
+SETD2
+RHOA
+BAP1
+PBRM1
+MITF
+EPHA3
+POLQ
+MRAS
+PIK3CB
+FOXL2
+ATR
+MECOM
+TBL1XR1
+PIK3CA
+SOX2
+DCUN1D1
+MAP3K13
+ETV5
+EIF4A2
+FGF12
+TFRC
+CRIPAK
+FGFR3
+PDGFRA
+KIT
+KDR
+FGF5
+FAM175A
+TET2
+FGF2
+INPP4B
+FBXW7
+BRD9
+TERT
+LIFR
+RICTOR
+PRKAA1
+FGF10
+MAP3K1
+PIK3R1
+MSH3
+RASA1
+APC
+FGF1
+PDGFRB
+NPM1
+FGFR4
+NSD1
+FOXC1
+HIST1H1C
+HIST1H2BD
+DDR1
+BRD2
+CDKN1A
+PIM1
+CCND3
+ROS1
+SGK1
+MYB
+ESR1
+ARID1B
+PMS2
+RAC1
+ETV1
+IL6
+NFE2L3
+EGFR
+HGF
+CDK6
+RELN
+PIK3CG
+MET
+SMO
+BRAF
+EPHB6
+EZH2
+RHEB
+KMT2C
+EGR3
+PPP2R2A
+NRG1
+FGFR1
+SOX17
+SGK3
+RSPO2
+RAD21
+DEPTOR
+MYC
+EPPK1
+JAK2
+RPS6
+CDKN2A
+CDKN2B
+GNAQ
+NTRK2
+PTCH1
+TLR4
+MAPKAP1
+CDK9
+ABL1
+TSC1
+BRD3
+NOTCH1
+GATA3
+MAP3K8
+RET
+ARID5B
+PTEN
+FGF8
+SMC3
+SHOC2
+FGFR2
+HRAS
+WEE1
+WT1
+MAPK8IP1
+MALAT1
+RPS6KB2
+CCND1
+FGF19
+FGF4
+FGF3
+PAK1
+ATM
+KMT2A
+CBL
+CHEK1
+CCND2
+FGF23
+FGF6
+PTPN6
+ETV6
+CDKN1B
+PIK3C2G
+KRAS
+H3F3C
+LRRK2
+IRAK4
+ARID2
+KMT2D
+ACVRL1
+ACVR1B
+ERBB3
+CDK4
+MDM2
+FRS2
+NAV3
+PTPN11
+TBX3
+PRKAB1
+HNF1A
+NCOR2
+POLE
+FGF9
+CDK8
+FLT3
+BRCA2
+RB1
+FGF14
+LAMP1
+GAS6
+AJUBA
+NKX2-1
+NKX2-8
+FOXA1
+RAD51B
+MLH3
+AKT1
+SPRED1
+MGA
+FGF7
+MAP2K1
+SIN3A
+IDH2
+IGF1R
+TSC2
+MLST8
+PDPK1
+PALB2
+MAPK3
+CBFB
+CTCF
+CDH1
+PHLPP2
+TP53
+MAP2K4
+NCOR1
+TIAF1
+NF1
+RAD51D
+CDK12
+ERBB2
+RARA
+TOP2A
+STAT3
+BRCA1
+ETV4
+SPOP
+VEZF1
+MIR142
+RAD51C
+RPS6KB1
+BRIP1
+GNA13
+AXIN2
+SOX9
+RPTOR
+PIK3C3
+SETBP1
+SMAD2
+SMAD4
+PHLPP1
+STK11
+GNA11
+MAP2K2
+KEAP1
+SMARCA4
+BRD4
+JAK3
+PIK3R2
+CCNE1
+TSHZ3
+CEBPA
+KMT2B
+AKT2
+PRX
+ERCC2
+ERCC1
+ARHGAP35
+AKT1S1
+POLD1
+PPP2R1A
+CSNK2A1
+FKBP1A
+FOXA2
+BCL2L1
+ASXL1
+SGK2
+TSHZ2
+ZNF217
+GNAS
+U2AF1
+RUNX1
+ERG
+TMPRSS2
+U2AF1
+CRKL
+MAPK1
+SMARCB1
+CHEK2
+EWSR1
+NF2
+MYH9
+EP300
+CYP2D6
+PIM3
+USP9X
+KDM6A
+RBM10
+ARAF
+ERAS
+PIM2
+KDM5C
+SMC1A
+AMER1
+AR
+MED12
+TAF1
+ATRX
+AGTR2
+STAG2
+PHF6
+SRY