TITLE: nf-vcf-novel-dataset-builder
AUTHORS: Israel Aguilar Ordoñez

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Nextflow pipeline used to build the novel variants dataset for the 100GMX project.</div><div class = "text-block">'nf-vcf-novel-dataset-builder' is a pipeline tool that builds a VCF file compiling only novel variants according to dbSNP and VEP, from a VEPextended annotated VCF file. This novel selection does not include singletons and private variants. The main output is in VCF format. Additional outputs include the dataset in TSV format, and a sequence coverage from gnomAD in these sites.</div><div class = "text-block"><span>Important note: input file must be previously annotated by</span><a href="https://github.com/Iaguilaror/nf-VEPextended" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://github.com/Iaguilaror/nf-VEPextended</span></a></div><div class = "text-block">All steps described are mk modules of code that will be done automatically through Nextflow pipeline. </div></div>

[STEPS]
?. [Pre-processing]
Remove singletons and privateRemove singletons and private variants.Dependencies:
a) Filter positions where AC >= '3' to eliminate singletons and private.* AC could be modified.
?. [Core-processing]
Select novelSelect novel SNPs, indels variants and concatenate both type variants.Dependencies:
a) Filter novel SNPs.b) Filter novel indels.c) Concatenate novel SNPs and indels.d) Sort VCF.
?. [Pos-processing]
Count per sampleList and count samples to present block data in a column format.final-counter.R is a tool for transforming wide to long format. Dependencies: final-counter.RDependencies:
a) List all samples.b) Extract block of counted data only.c) Transform to column format.
?. [Pos-processing]
Simplify VCF for dbSNP uploadRemove genotypes, remove FORMAT and all INFO field except INFO/AF and FORMAT, also changes AF to AF_natmx.Dependencies:Final Output:#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO chr21   5227536 .       C       CTCTCCTCTCT     .       .       AF_natmx=0.019 ...
a) Remove genotypes.b) Remove fields except for INFO/AF and FILTER.c) Rename local AF to AF_natmx, also in the header.
A compressed and simplified VCF file format.Example line(s):
?. [Pos-processing]
VCF2TSVConvert vcf to tsv format.Dependencies:Final Output:CHROM   POS     REF     ALT     AF_natmx        Allele  Consequence     IMPACT  SYMBOL  Gene    Feature_type    Feature BIOTYPE EXON    INTRON  HGVSc   HGVSp   cDNA_position   CDS_position    Protein_posi chr21   5227536 C       CTCTCCTCTCT     0.019   TCTCCTCTCT      intergenic_variant      MODIFIER        .       .       .       .       .       .       .       .       .       .       .       .       . ...
A compressed TSV file format.Example line(s):
?. [Pos-processing]
Consequence cataloguerCatalogue consequences for each type of variant.cataloguer.R is a tool for cataloging the consequences of novel variants.Dependencies:cataloguer.RDependencies:Final Output:Consequence     number_of_variants      Type    General_category        First_specific_consequence 3_prime_UTR_variant     2       noncoding       UTR     3 prime UTR 3_prime_UTR_variant&NMD_transcript_variant      NA      noncoding       UTR     3 prime UTR ...
A compressed TSV file format by each category of variant and a SVG file.Example line(s) of TSV:
?. [Pos-processing]
Coverage gnomADPlot gnomAD coverages.coverage-analyzer.R is a tool for plotting coverage of the gnomAD project.Dependencies:coverage-analyzer.RDependencies:Final Output:
.tif file format by each variant category.