README.md
In daissi/MORFEE: Mutation on Open Reading FramE annotation

MORFEE (Mutation on Open Reading FramE annotation) is a tool (R package) that, from a VCF file, detects and annotates single nucleotide variants creating premature ATG codons.

MORFEE algorithm is written in R language and can run on all operating systems which have an R interpreter (including Linux, macOS and Windows). MORFEE starts with a minimal VCF file (i.e. with at least the chr, position, reference allele and alternate allele fields) as an input, but can also work with already ANNOVAR-annotated (Wang et al., 2010) VCF files. MORFEE has some R packages dependencies which are available on CRAN or Bioconductor repositories and uses the GENCODE database.

When using MORFEE, please cite our publication.

Not yet available!

library("devtools")
install_github("daissi/MORFEE")

In a first step, MORFEE reads the input VCF file and use ANNOVAR (that has then to be beforehand installed) through the wrapper function vcf.annovar.annotation to annotate all variants. This step is skipped if the input file has already been annotated. The minimal ANNOVAR annotations required by MORFEE are: - Func.refGene to extract 5'UTR variants. - GeneDetail.refGene to extract transcript ID.

# Annotation with ANNOVAR
table_annovar.pl \
        inst/extdata/VCF_example.vcf \
        ${PATH_ANNOVAR_DB} \
        -buildver hg19 \
        -remove -protocol refGene,gwasCatalog,avsnp150,clinvar_20190305,gnomad211_genome,dbnsfp35a \
        -operation gx,r,f,f,f,f -nastring . -vcfinput \
        -xref ${PATH_ANNOVAR_DB}/morfee.lof_metrics.by_gene.txt

library(VariantAnnotation)
library(MORFEE)

my_raw_vcf <- "inst/extdata/VCF_example.vcf"

# Annotation with ANNOVAR through the wrapper function
vcf.annovar.annotation(my_raw_vcf)

library("VariantAnnotation")
library("MORFEE")

# Download database and create an R object used by MORFEE
MORFEE_DATA <- get.morfee.data()

# To avoid too much Internet traffic, save locally this object
# save(MORFEE_DATA, file="MORFEE_DATA.RData")
# load("MORFEE_DATA.RData")

MY_VCF <- "VCF_example.hg19_multianno.vcf"

# Read/Load the VCF into R
my_vcf <- readVcf(MY_VCF)

# Perform the MORFEE annotation
my_vcf_morfee <- morfee.annotation(my_vcf, MORFEE_DATA)

# Keep only variants which create a new upstream ATG sequence
my_vcf_morfee_NEW <- my_vcf_morfee[!is.na(info(my_vcf_morfee)$MORFEE)]

# Write a VCF file with the new MORFEE field/annotation
writeVcf(my_vcf_morfee_NEW, filename="VCF_example.hg19_multianno.morfee_anno_NEW.vcf")

# Write an XLSX file with the new MORFEE field/annotation
vcf_2_xlsx(my_vcf_morfee_NEW, file="VCF_example.hg19_multianno.morfee_anno_NEW.xlsx")

Please see below the description of the different columns of the xlsx file: - GeneDetail.refGene: Sequence Variant Nomenclature (ANNOVAR output). Please note, this nomenclature does not respect the HGVS Recommendations (doi:10.1002/humu.22981). The position of the variant used with a prefix c. should be the position of the variant regarding the ATG position based one the coding sequence. In other words, the position on a sequence WITHOUT introns. ANNOVAR reports the position on the sequence WITH introns. - orfSNVs_type: uATG or uSTOP to determine whether there is a creation of an upstream ATG or a deletion of an upstream STOP. - orfSNVs_frame: in_frame or out_of_frame to determine whether there is a frame shift between the new ATG (or deleted STOP) and the reference ATG. - orfSNVs_position: overlapping, not_overlapping or elongated_CDS to determine the position of the predicted ORF to the reference protein. - Ratio_length_pred_obs: ratio between the predicted vs the observed length of the protein (<1 for a shorter protein and >1 for a longer protein). In case of several transcripts, only one value is given. That corresponding to the predicted length the closest to the observed length, i.e the ratio closest to 1. - NewAALength: predicted length of the new protein in amino acids. - MORFEE_ATG: MORFEE VCF-style annotation for variants creating new uATG. - MORFEE_STOP: MORFEE VCF-style annotation for variants deleting uSTOP.

All fields below come from ANNOVAR annotation:

pLI.refGene: probability of Loss-of-function Intolerance score from gnomAD
exp_lof.refGene: expected predicted Loss-of-Function variants from gnomAD
oe_lof.refGene: observed / expected score
oe_lof_lower.refGene: lower limit of 90% confidence interval of oe metric
oe_lof_upper.refGene: upper limit of 90% confidence interval of oe metric
gwasCatalog: gene-associated phenotype from GWAS Catalog
CLNDN: disease name from ClinVar
CLNDISDB: database name and identifier for the disease name from ClinVar
CLNSIG: clinical significance from ClinVar
AF: allele frequency from gnomAD
AF_popmax: maximum population allele frequency from gnomAD
SIFT_pred: Sorting Tolerant From Intolerant function prediction from dbNSFP
Polyphen2_HDIV_pred: Polyphen2 function prediction based on HumDiv from dbNSFP
Polyphen2_HVAR_pred: Polyphen2 function prediction based on HumVar from dbNSFP
LRT_pred: Likelihood Ratio Test function prediction from dbNSFP
MutationTaster_pred: MutationTaster function prediction from dbNSFP
MutationAssessor_pred: MutationAssessor function prediction from dbNSFP
FATHMM_pred: Functional Analysis through Hidden Markov Models function prediction from dbNSFP
PROVEAN_pred: Protein Variation Effect Analyzer function prediction from dbNSFP
MetaSVM_pred: Support Vector Machine combination of function prediction score from dbNSFP
MetaLR_pred: Logistic Regression combination of function prediction score from dbNSFP
M.CAP_pred: Mendelian Clinically Applicable Pathogenicity likelihood score from dbNSFP
REVEL_rankscore: Rare Exome Variant Ensemble Learner pathogenicity score from dbNSFP
MutPred_rankscore: pathogenicity score from dbNSFP
CADD_phred: Combined Annotation Dependent Depletion pathogenicity score from dbNSFP
fathmm.MKL_coding_pred: fathmm-MKL function prediction based on HumDiv from dbNSFP
integrated_fitCons_score: fitCons function prediction based on HumDiv from dbNSFP
GERP.._RS: GERP++ RS conservation score from dbNSFP
phyloP100way_vertebrate_rankscore: phyloP conservation score from dbNSFP
phyloP20way_mammalian_rankscore: phyloP conservation score from dbNSFP
phastCons100way_vertebrate_rankscore: phastCons conservation score from dbNSFP
phastCons20way_mammalian_rankscore: conservation score from dbNSFP
SiPhy_29way_logOdds: SiPhy conservation score from dbNSFP