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#annotation-pipeline

This pipeline annotates a txt input file containing min 5 columns ("Chr\tStart\tEnd\tRef\tAlt") with the following annotations.

####[ANNOVAR] [ANNOVAR]: http://annovar.openbioinformatics.org/en/latest/

• Func.refGene: Tells whether the variant hit exons or hit intergenic regions, or hit introns, or hit a non-coding RNA genes.
• Gene.refGene: If the variant is exonic/intronic/ncRNA, this column gives the gene name (if multiple genes are hit, comma will be added between gene names); if not, the column will give the two neighboring genes and the distance to these neighboring genes.
• GeneDetail.refGene:
• ExonicFunc.refGene: Tells the functional consequences of the variant (possible values in this fields include: nonsynonymous SNV, synonymous SNV, frameshift insertion, frameshift deletion, nonframeshift insertion, nonframeshift deletion, frameshift block substitution, nonframshift block substitution)
• AAChange.refGene: Gene name, the transcript identifier and the sequence change in the corresponding transcript.
• cytoBand: Cytogenic band.
• snp138: dbsnp138 annotation. if present then rs id will be present else -1

####[Frequencies from 1000 genome new release] [Frequencies from 1000 genome new release]: http://www.1000genomes.org/category/frequently-asked-questions/population

• 1000g2014oct_all: All Individuals from the October 2014 release
• 1000g2014oct_eur: European Individuals from the October 2014 release
• 1000g2014oct_afr: African Individuals from the October 2014 release
• 1000g2014oct_amr: Ad Mixed American Individuals from the October 2014 release
• 1000g2014oct_eas: East Asian Individuals from the October 2014 release
• 1000g2014oct_sas: South Asian Individuals from the October 2014 release

####[NHLBI] [NHLBI]: http://evs.gs.washington.edu/EVS/

• esp6500_all: All 6503 Individuals
• esp6500_ea: European American
• esp6500_aa: African American

####[ExAC] Exome Aggregation Consortium Data. v0.3 nonTCGA data [ExAC]: http://exac.broadinstitute.org/

• ExAC_ALL_nonTCGA: Excluding TCGA cohorts (53,105 samples)
• ExAC_AFR_nonTCGA:
• ExAC_AMR_nonTCGA:
• ExAC_EAS_nonTCGA:
• ExAC_FIN_nonTCGA:
• ExAC_NFE_nonTCGA:
• ExAC_OTH_nonTCGA:
• ExAC_SAS_nonTCGA:

####[cg69] Frequency in 69 samples sequenced at Complete Genomics
[cg69]: http://www.completegenomics.com/public-data/69-genomes/ ####[nci60] Frequency in 60 Cell lines sequenced at NCI
[nci60]: http://discover.nci.nih.gov/cellminer/home.do ####[ExAC] Exome Aggregation Consortium Data. v0.3 [ExAC]: http://exac.broadinstitute.org/

• ExAC_ALL: All Individuals (60,706 samples)
• ExAC_AFR: African
• ExAC_AMR: American
• ExAC_EAS: Eastern Asian
• ExAC_FIN: Finnish
• ExAC_NFE: Non-Finnish Europian
• ExAC_OTH: Other
• ExAC_SAS: South Asian

####[ClinSeq] [ClinSeq]: http://www.genome.gov/20519355

• Clinseqc_genotypes: The number of genotypes with MPG score >=10.
• Clinseqc_homref: Number of genotypes where all alleles seen are the reference allele (I.e., if haploid, one reference allele, and if diploid, two reference alleles).
• Clinseqc_het: Number of diploid genotypes for which one allele is the reference allele, and the other is the variant allele .
• Clinseqc_homvar: Number of genotypes where all alleles seen are the variant allele (I.e., if haploid, one copy of the variant allele, and if diploid, two copies of the variant allele).
• Clinseqc_hetnonref: Number of diploid genotypes for which one allele is the variant allele, and the other is a third allele that is not the reference and not the variant allele.
• Clinseqc_other: Any genotype that cannot be categorized into one of the above categories, including haploid third alleles (which are non-reference and not the variant allele), diploid homozygous third alleles and diploid heterozygous genotypes which do not contain the variant allele.
• Clinseqc_refallele: Number of reference alleles observed in genotypes with MPG score >=10. Haploid homref and diploid het genotypes will contribute one copy, while diploid homref genotypes will contribute two to this count.
• Clinseqc_varallele: Number of variant alleles observed in genotypes with MPG score >=10. Haploid homnonref and diploid het and hetnonref genotypes will contribute one copy, while diploid homnonref genotypes contribute two to this count.
• Clinseqfreq_homref: Frequency of homozygous reference genotypes.
• Clinseqfreq_het: Frequency of heterozygous genotypes where the reference is one of the alleles.
• Clinseqfreq_homvar: Frequency of homozygous non-reference genotypes.
• Clinseqfreq_hetnonref: Frequency of heterozygous genotypes where the reference is not one of the alleles.
• Clinseqfreq_refallele: Frequency of the reference allele.
• Clinseqfreq_varallele: Frequency of the variant allele.
• Clinseqref_is_minor: Flag 1 if the reference is the minor allele.
• Clinseqc_major: The number of major alleles, which can be either the reference or the variant allele.
• Clinseqc_minor: The number of minor alleles, which can be either the reference or the variant allele.
• Clinseqmaf: The frequency of the minor allele compared to the sum of all alleles.
• Clinseqchisquare: The chi-square value (NOT p-value) calculated using the genotypes AA, Aa, aa where A is the major allele and a is the minor allele (major and minor can only be reference or variant)

####[CADD] [CADD]: http://cadd.gs.washington.edu/

• CADD: Combined Annotation Dependent Depletion (CADD) Score
• CADD_Phred: Combined Annotation Dependent Depletion (CADD) Score

####[SIFT] [SIFT]: http://sift.jcvi.org/

• SIFT Prediction:
  Prediction from SIFT (DAMAGING, TOLERATED, Not scored, Damaging due to stop, N/A, DAMAGING *Warning! Low confidence.)
• SIFT Score:
  0 = DAMAGING,
  1 = TOLERATED,
  N/A = Damaging due to stop, Not scored, N/A

####[PolyPhen-2] [PolyPhen-2]: http://genetics.bwh.harvard.edu/pph2/

• PPH2 Prediction:(benign, possibly damaging, probably damaging)
• PPH2 Class: (neutral, deleterious)
• PPH2 Probability: (neutral, deleterious)

####[clinvar_20150330] [clinvar_20150330]: http://www.ncbi.nlm.nih.gov/clinvar/

####[cosmic70] [cosmic70]: http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

####[HGMD] [HGMD]: https://portal.biobase-international.com/hgmd/pro/global.php#other NIH Users can create account and access the database [here]. Enter the code 1881-6975-97565225 in the license field during the account registration process. [here]: https://portal.biobase-international.com/cgi-bin/portal/login.cgi

• hgmd_Acc-No: hgmd Acc Number
• hgmd_Category: Category as defined by hgmd.
• hgmd_GeneName: Gene Name
• hgmd_Phenotype: Associated Disease

####[MATCH] Trial
[MATCH]: http://www.cancer.gov/about-cancer/treatment/clinical-trials/nci-supported/nci-match

• MATCH_ArmID: Name of the MATCH Trial Treatment Arm.
  Details are available [here] [here]: https://matchbox.nci.nih.gov/matchbox/views/treatmentArmsDetails.html?treatmentArmId=EAY131-A&treatmentArmsList=true

####[DoCM] Database of Curated Mutations
[DoCM]: http://docm.genome.wustl.edu/

• DoCM Disease: Name of the cancer type
• DoCM PMID: PubMed ID

####[canDL] Cancer Driver Log
[canDL]: https://candl.osu.edu/browse

• CanDL_Diagnosis Diagnosis as listed on the server
• CanDL_Level_of_Evidence Level of evidence.
  Tier 1: Alteration has matching FDA approved or NCCN recommended therapy
  Tier 2: Alteration has matching therapy based on evidence from clinical trials, case reports, or exceptional responders.
  Tier 3: Alteration predicts for response or resistance to therapy based on evidence from pre-clinical data (in vitro or in vivo models)
  Tier 4: Alteration is a putative oncogenic driver based on functional activation of a pathway
• CanDL_PMIDs PubMed ID

####[TCC] Targated Cancer Care
[tcc]: https://targetedcancercare.massgeneral.org/

• targated_cancer_care.Gene Gene Name
• targated_cancer_care.AA Amino Acid Change

####[My Cancer Genome]
[My Cancer Genome]: http://www.mycancergenome.org/

• MyCG_Gene: Name of the gene
• MyCG_Codon: Codon change in database
• MyCG_cDNA Change: cDNA change in database
• MyCG_Link(s): Link to the page data is extracted from
• This update does not contain the name of diagnosis as annotation but it contains the link to the website which can give much more detail information about the mutation
• Because the genomic changes are based on backlocation; the cDNA change in database and the mutation in question may not be same.

####[CIViC] Clinical Interpretation of Variants in Cancer
[CIViC]: https://civic.genome.wustl.edu/#/home

• civic_PMID: PubMed ID
• civic_Rating:
• civic_EvidenceLevel:
• civic_Diagnosis:

####ICGC, TCGA and Pediatric NextGen Studies.

** Pediatric Studies Log **

ICGC_09202015
TCGA_07142015
ALL_22237106
ALL_22897843
ALL_22897847
ALL_23212523
ALL_23334668
AML_23153540
DIPG_22661320
EPEN_24553141
EPEN_24553142
ETMR_24316981
EWS_25010205
EWS_25186949
EWS_25223734
GBM_18772396
GBM_23079654
HEP_23887712
HGG_20068183
HGG_22286061
HGG_22286216
HGG_23417712
HGG_24705250
HGG_24705251
LGG_23104868
LGG_23222849
LGG_23583981
MED_21163964
MED_22265402
MED_22722829
MED_22722829_G
MED_22832583
MIX_24055113
MIX_24710217
MRT_22797305
NBL_22142829
NBL_22367537
NBL_22416102
NBL_23202128
NBL_23334666
NBL_24147068
NBL_25517749
NBL_26121087
NEO_22187960
OST_24703847
OST_25512523
RB_22237022
RB_24688104_G
RMS_22142829
RMS_24272621
RMS_24332040
RMS_24436047
RMS_24436047_T
RMS_24793135
RMS_24824843
RMS_26138366
SAR_20601955
UVM_TCGA
WT_24909261
WT_25190313
WT_25313908
WT_25670082
And data downloaded from FoundationMedicine

####57 [ACMG] genes and the pertinent information. [ACMG]:https://www.acmg.net/docs/ACMG_Releases_Highly-Anticipated_Recommendations_on_Incidental_Findings_in_Clinical_Exome_and_Genome_Sequencing.pdf

• Gene.refGene
• ACMG_Disease
• ACMG_Age-to-Report
• ACMG_Gene-Reviews-PubMedID
• ACMG_Inheritance
• ACMG_Known-vs-Expected
• ACMG_LSDB

perl annotation-pipeline.pl -infile <NameOfYourFile>