Scripts and data files used for the annotation of 3'UTR and microRNA variants
The perl script pipeline_joint_V2.pl performs a detailed annotation of VCF file. usage: perl pipeline_joint_V2.pl VCFfile cohortName The script is based havily on annovar (https://doc-openbio.readthedocs.io/projects/annovar/en/latest/). Annovar scripts have to be placed under folder "annovar". The following files have to be downloaded from annovar site and to be placed under annovar/humandb: refGene,avsnp144,1000g2014oct_eur,esp6500siv2_ea,cg69,phastConsElements46way,genomicSuperDups,dbnsfp30a, wgEncodeRegDnaseClustered,wgEncodeRegTfbsClustered,clinvar_20150629,exac03
Our special annotation for microRNA and 3UTR variants: targetScanS,preMiRNA,matureMiRNA,seedMiRNA,TargetS16_conSites_poorConsFam,TargetS16_nonconsvSites_consvFam TargetS16_noncosvSites_broadConsFam,TargetS16_sites,GenCode3UTR The files PITA_Ts_run and PITA_top_f- include prediction of miRNA binding site loss using PITA, performed on a restricted list of ALS related genes. GenCode3UTR- annotates specifically the 3UTRs of ALS related genes. The script also scans a file called eXome_db which contains variations of the Israeli population. The online version contains dummy information due to ethical reasons.
On top of that, the script is searching for a gain of miRNA binding site due to a mutation in the 3UTR. For that, the script extracts the sequence sorrunding the mutation site from the human genome. For that it expects to find a file called human_g1k_v37.fasta at the script folder. Importantly, it is designed to work with the GATK human genome, i.e. chromosome identifiers: 1, 2, 3 ect. and not chr1, chr2, chr3 ...ect. Additional scripts: GenotypeToSummary.pl Finding which individuals carry specific mutations
filter_annotation_file.pl Removes multi-allelic variants from the annotation file