Shore methyl
From SHORE wiki
shore methyl quantifies methylated and unmethylated cytosines from BS-seq alignments (only genomemapper).
Command line options
Usage: shore methyl [OPTIONS]
| Mandatory | ||
| -n STRING | Name (any of species, strain, accession, project or any other ID) | |
| -f STRING | Reference genome sequence from the IndexFolder, *.shore file | |
| -o STRING | AnalysisFolder, will be created | |
| -i STRING[,...] | Shore directories or map.list file(s) | |
| -g INT | Core offset - do not trust the first and last -g positions of the alignment. default: max MM's
Short read alignments are prone to misalignments towards the ends of the read. This value specifies how many bases at each end will be regarded as suspicious. | |
| Quality threshold | ||
| -q INT | (Default: 5) | Cutoff for base masking using Sanger calibrated qualities |
| -c INT | Cutoff for base masking using chastity values | |
| Basecalling (scoring matrix approach) | ||
| -a STRING | Scoring matrix file (recommended, activates new basecalling approach) | |
| -b FLOAT | (Default: 0.2) | Minimum allele frequency of alternative base call |
| Basecalling (decision tree approach) | ||
| -x INT | (Default: 3) | Minimum coverage threshold |
| -m INT | (Default: 3) | Maximum observed to expected coverage |
| -e FLOAT | (Default: 0.1) | Minimum observed to expected coverage |
| -y FLOAT | (Default: 0.8) | Minimum concordance of homozygous SNPs (0 to 1) |
| -d FLOAT | (Default: 0.67) | Minimum concordance of homozygous Indels |
| -t FLOAT | (Default: 0.25) | Minimum frequency for heterozygous pos (0 to 1) |
| -u FLOAT | (Default: 0.02) | Minimum frequency for minor allele pos (0 to 1) |
| -z INT | (Default: 10) | Quality threshold, max base quality |
| Optional | ||
| -v | Create additional output files containing all intermediate data | |
| -r | Graphical output of statistics using R | |
