Shore merge
From SHORE wiki
shore merge merges and filters alignment files.
Command line options
Usage: shore merge [OPTIONS] [ALIGNMENT_PATHS]
| Input | ||
| -m, --infiles=<arg[,...]> | Alignment files or shore directories (run, lane, read or sample; comma-separated; defaults to <outdir>) | |
| -I, --idordered | Input alignments are sorted by read ID and not by coordinate | |
| Main output options | ||
| -o, --outdir=<arg> | (Default: AlignmentFolder) | Set output directory (will be created if necessary) |
| -A, --no-alignments | Deactivate processing of alignment files (only merge insert size distributions or left over files) | |
| -l, --leftovers | Activate merging of leftover reads | |
| -p, --rplot | Graphical output of statistics using R | |
| Ancillary output options | ||
| -s, --subsamples=<arg[,...]> | Generate random subsamples of <arg> reads | |
| --diff | Write all reads that only occur in a single alignment file | |
| --phasesplit=<arg> | Split reads by <arg>-mer phasing | |
| --combine | Combine alignments (discard duplicate entries and alignments that are not the best hit) | |
| -q, --stats-only | Statistics only, do no write the merged data | |
| -t, --no-stats | Disable alignment statistic | |
| -Z, --nocompress | Do no compress output files | |
| -S, --stdout | Don't create an output directory, write alignments to standard output (implies -t, -Z) | |
| Alignment filter | ||
| -H, --hits-range=<arg,arg> | Set the allowed range of repetitiveness ('1,1' = nonrep reads) | |
| -M, --mm-range=<arg,arg> | Set the allowed range of mismatches | |
| -R, --region=<arg> | Only use reads that overlap with the range [chr1:pos1..[chr2:]pos2] | |
| --assume-length=<arg> | (Default: 400) | Assume maximal alignment length <arg>, enables fast range queries |
| -X, --p3fix=<arg> | Set the 3' end to a fixed distance from the 5' end | |
| -N, --read-lengths=<arg[,...]> | Use only reads of the given length(s) | |
| -T, --strand=<arg> | Use only reads from the given strand | |
| -B, --duplicates=<arg> | Report at maximum <arg> reads with the 5' end at the same position on the same strand | |
| --wpoiss=<arg> | Window size for adaptive duplicate read filtering | |
| --sam-ref=<arg> | Reference sequence for SAM file parsing | |
| --peflags=<arg[,...]> | Use only reads with the given PE flag(s) | |
| Leftover filter | ||
| --badqual=<arg> | (Default: 10) | Quality threshold |
| --maxbadbases=<arg> | (Default: 8) | Max. number low quality bases |
