Man pages for mmaitenat/ideafix
ideafix, DEAmination FIXing
| annotate_deaminations | Annotate deaminations to file |
| calc_SB_GATK | Calculate GATK strand bias |
| calc_SB_Guo | Calculate Guo strand bias |
| check_algorithm | Check classification algorithm name |
| check_arguments | Check required arguments exist |
| check_descriptors | Check available descriptors |
| check_lowercase | Check case |
| classify_variants | Classify variants as deaminations or non-deaminations |
| classify_variants_RF | Classify variants as deaminations or non-deaminations with... |
| classify_variants_XGBoost | Classify variants as deaminations or non-deaminations with... |
| extract_fa | Retrieve descriptors from fasta file |
| extract_vcf | Retrieve descriptors from vcf file |
| get_AF | Retrieve allele frequency |
| get_alt_allele | Retrieve alternate allele |
| get_alt_bases | Retrieve number of alternate alleles |
| get_base_qual | Retrieve base quality |
| get_depth | Retrieve read depth |
| get_descriptors | Get variant descriptors |
| get_fraglength | Retrieve variant median fragment length |
| get_map_qual | Retrieve mapping quality |
| get_mut_id | Retrieve mutation id |
| get_pos_from_end | Retrieve variant distance from end of read |
| get_ref_allele | Retrieve reference allele |
| get_ref_bases | Retrieve number of reference alleles |
| get_RPOB | Calculate read pair orientation bias |
| get_samplename | Retrieve sample name |
| get_SB | Calculate strand bias |
| get_surr_bases | Retrieve surrounding base sequence of locus |
| ideafix | ideafix, DEAmination FIXing Package |
| join_uncompress_targz | Join and uncompress tar.gz files |
| one_hot_encoding | oneHotEncoding |
| run_ideafix | Classify variants |
| write_region_file | Write temporary loci region file |
| write_vcf | Annotate deaminations in input vcf file |
