Man pages for manzomonza/auto-ngs-annotation
Editing, Parsing And Annotation of ThermoFisher IonReporter and Genexus Precision NGS Results
| activityList_format | Output single string of variants from detected SNVs and CNVs |
| addMissingCols | Add missing columns to make inconsistent IR output work |
| allelecolumnCheck | Allele column check |
| amino_acid_conversion_one_to_three | ###### Change one letter to three letter code |
| amino_acid_conversion_three_to_one | ###### Change three to one letter code |
| annotateWatchdogTables | ### Annotate files in watchdog folder |
| bimiMatchUp | Match Variant with BIMI table |
| checkTSG | Check if Gene is TSG and if variant leads to Ter or... |
| ClassficationDe | Translate clinvar clinical significance to german |
| ClassficationFr | Translate clinvar clinical significance to french |
| clinvarCheck | Check, download and update Clinvar Summary Table (from NIH)... |
| clinvarSingleRow | Edit single variant |
| clinvarTableOutput | Combine single edited variants into table |
| cnvAnnot | Annotate CNVs |
| cnvParse | Separates CNV confidence column in non-precision panels |
| complex_one_to_three | #### Complex One To Three AA switch |
| cosmic_counter_per_table_element | Applies counter_cosmic_variant_tissue rowwise to SNV table |
| cosmic_counter_wrapper | Wrapper function for COSMIC tissue count |
| cosmic_sql_search | Count variant occurences per tissue in COSMIC db |
| counter_cosmic_variant_tissue | Count variant occurences per tissue in COSMIC db#' |
| count_variants_per_panel | Output counts of variants per panel only SNVs for now |
| cp_mv_gnxs | COPY and rename GNXSinfo to GNXS_metadata |
| create_output_files | #### Function to write out tables create_output_files... |
| diagnose_D_F_columns_snv | ## Prepare Diagnosis column in German and French to be... |
| exonAnnot | ### ExonAnnot |
| extract_snv_position | Extract position of SNVs |
| fsClinvarfix | Frameshift clinvar fix |
| fusionInfoParser | Parse Fusion info |
| FusionOutput | Generate Combined output file for Fusion.tsv |
| fusionParser | Parses Precision RNA Fusion.tsv |
| gene_symbol_sub | Substitute comma separated gene symbols with single gene name |
| gene_symbol_sub_table | Substitute gene symbols |
| info_cancerHotspots | Retrieve if variant codon position is covered in... |
| infoName | Extract Sample name information from Genexus/Precision... |
| make_output_tables | Generate tables to export |
| make_output_tables_precision | Generates output tables for precision |
| mtbpFormat | Ouput Karolinska MTBP compliant output |
| mult100 | Multiply by 100 or not |
| oneORthree_code | Single or three letter code |
| one_three_aa_precision | ####### Simple One To Three AA amino acid switch, used in... |
| orderSignificance | Order by clinical significance |
| percentParse | Percent Frequency parsing |
| precisionPipeline_TableOutput | ## Output Tables pipelines |
| prep_chr | Convert coding and location in prep_snv.txt to gnomad... |
| prep_filepaths | From filepath to watchdog/prep filepaths |
| readIn | Read in files |
| read_rename_select | read in, rename and select |
| read_rename_select_precision_snv | Read rename select for GNXS files |
| renameCol | Renaming of inconsistently named columns |
| row_activityList_format_cnv | Output concatenated string of gene, copy number and... |
| row_activityList_format_snv | Output concatenated string of gene, change and allele... |
| saveReport_xlsx | Save report to XLSX file |
| shortenFilename | Shorten filename |
| snvParse | SNV PARSE Takes SNV part of IR output and converts entry with... |
| splicesite_Annot | ### splice site annotation Function to interrogate if variant... |
| splicesite_rowwise | Rowwise splice site annotation |
| std_metadataCollector | Collects Metadata and writes out table This function extracts... |
| stdPipeline_TableOutput | Pipeline from intro file to Watchdog output files. These... |
| tsgParseTable | tsgParseTable Checks SNV contains 'fs' or 'Ter' |
| wrapper_row_cancerHotspots | Apply cancerhotspot check to single row |
| wrapper_table_cancerHotspots | Apply cancerhotspot check to snv_variant table |
