CHERIPIC /full_path_to/cheripic -v output_log.txt ]]> vcf bam pileup info warnings debug back cross out cross polyploidy == "true"

**Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC)** CHERIPIC is a ruby tool to pick causative mutation from bulk segregant sequencing ------ **What it does** This tool uses ``cheripic`` tool to analyse bulk segregant sequencing to identify causative muation .. class:: infomark Provides a list of snps that could either closely linked markers or the causative mutation. ------ **Input formats** assembly file should be a fasta file used for generating pileups from bulks bulk alignment files should be pileup files ------ **Outputs** The output is a text file, and has the following columns:: Column Description ----------------- -------------------------------------------------------- 1 HME_Score Homozygosity Enrichment score 2 AlleleFreq Allele frequency 3 seq_id Contig/Scaffold id 4 position 1-based index of the position in contig 5 ref_base Reference nucleotide at the position 6 coverage read depth 7 bases read bases 8 base_quals read base qualities 9 sequence_left selected size of reference sequence on the left variant 10 Alt_seq Alternate allele at the position 11 sequence_right selected size of reference sequence on the right variant ------ **cheripic settings** All of the options have a default value. You can change any of them. All of the options are implemented. ------ **cheripic parameter list** OPTIONS: -f, --assembly Assembly file in FASTA format -F, --input-format bulk and parent alignment file format types - set either pileup or bam or vcf (default: pileup) -a, --mut-bulk Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1 --mut-bulk-vcf vcf file for variants from mutant/trait of interest bulk 1 -b, --bg-bulk Pileup or sorted BAM file alignments from background/wildtype bulk 2 --bg-bulk-vcf vcf file for variants from background/wildtype bulk 2 --output custom name tag to include in the output file name (default: cheripic_results) --loglevel Choose any one of "info / warn / debug" level for logs generated (default: debug) --hmes-adjust factor added to snp count of each contig to adjust for hme score calculations (default: 0.5) --htlow lower level for categorizing heterozygosity (default: 0.2) --hthigh high level for categorizing heterozygosity (default: 0.9) --mindepth minimum read depth at a position to consider for variant calls (default: 6) --max-d-multiple multiplication factor for average coverage to calculate maximum read coverage if set zero no calculation will be made from bam file. setting this value will override user set max depth (Default: 5) --maxdepth maximum read depth at a position to consider for variant calls if set to zero no user max depth will be used (default: 0) --min-non-ref-count minimum read depth supporting non reference base at each position (default: 3) --min-indel-count-support minimum read depth supporting an indel at each position (default: 3) --ambiguous-ref-bases including variant at completely ambiguous bases in the reference -q, --mapping-quality minimum mapping quality of read covering the position (default: 20) -Q, --base-quality minimum base quality of bases covering the position (default: 15) --noise praportion of reads for a variant to conisder as noise (default: 0.1) --cross-type type of cross used to generated mapping population - back or out (default: back) --use-all-contigs option to select all contigs or only contigs containing variants for analysis --include-low-hmes option to include or discard variants from contigs with low hme-score or bfr score to list in the final output --polyploidy Set if the data input is from polyploids -p, --mut-parent Pileup or sorted BAM file alignments from mutant/trait of interest parent (default: ) -r, --bg-parent Pileup or sorted BAM file alignments from background/wildtype parent (default: ) -R, --repeats-file repeat masker output file for the assembly (default: ) --bfr-adjust factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05) --sel-seq-len sequence length to print from either side of selected variants (default: 50) ------ .. class:: infomark **Tool Author** Shyam Rallapalli spaceholder