Shore qVar
From SHORE wiki
shore qVar computes consensus sequence, SNPs, indels and CNVs from alignments.
Command line options
Usage: shore qVar 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 | |
| -i STRING[,...] | Merged map.list file(s) or shore directories. | |
| -s STRING | Scoring matrix (found in shore/Analysis/scoring_matrix) | |
| -o STRING | AnalysisFolder, will be created. | |
| Assay type | ||
| -g | Genomic (turned on by default) | |
| -e | Exome enrichment (or any enrichment) assays | |
| -t | Quantitative sequencing (RNA-seq, ChIP-seq, DNaseI-seq etc.) | |
| Consensus prediction parameters | ||
| -c INT | (Default: 1) | Minimum coverage to attempt consensus base calling (Ref or SNP) at a position. |
| -d INT | (Default: 2) | Minimum allele coverage to attempt indel calling at a position. |
| -C INT | (Default: 999999) | Maximum coverage to attempt consensus base/indel calling at a position. |
| -r INT | (Default: 3) | Maximum repetitiveness (average hits) allowed for consensus base/indel calling. |
| -q INT | (Default: 5) | Minimum base quality (low quality bases are masked before consensus base calling. |
| -Q INT | (Default: 10) | Minimum consensus base/indel quality for reported calls. |
| -a FLOAT | (Default: 0.2) | Minimum allele frequency of reported calls. |
| -A INT | (Default: 2) | Minimum allele read support of reported calls |
| -b INT | (Default: 4) | Core offset - do not trust the first and last -b positions of an alignment. |
| Optional input files | ||
| -E STRING | Segment wise (e.g. exon) mean coverage file produced by 'shore count'. | |
| Consensus output | ||
| -x | No CNV prediction (improves speed; always off for exome or transcriptome seq) | |
| -y | Graphical output of statistics using R. | |
| -v | Do not remove intermediate output files. | |
