Program options for samtools_sort: sort: unrecognized option '--help' Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ---------------------------------------------- Program options for minimap2: Usage: minimap2 [options] | [query.fa] [...] Options: Indexing: -H use homopolymer-compressed k-mer (preferrable for PacBio) -k INT k-mer size (no larger than 28) [15] -w INT minimizer window size [10] -I NUM split index for every ~NUM input bases [4G] -d FILE dump index to FILE [] Mapping: -f FLOAT filter out top FLOAT fraction of repetitive minimizers [0.0002] -g NUM stop chain enlongation if there are no minimizers in INT-bp [5000] -G NUM max intron length (effective with -xsplice; changing -r) [200k] -F NUM max fragment length (effective with -xsr or in the fragment mode) [800] -r NUM bandwidth used in chaining and DP-based alignment [500] -n INT minimal number of minimizers on a chain [3] -m INT minimal chaining score (matching bases minus log gap penalty) [40] -X skip self and dual mappings (for the all-vs-all mode) -p FLOAT min secondary-to-primary score ratio [0.8] -N INT retain at most INT secondary alignments [5] Alignment: -A INT matching score [2] -B INT mismatch penalty [4] -O INT[,INT] gap open penalty [4,24] -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [2,1] -z INT[,INT] Z-drop score and inversion Z-drop score [400,200] -s INT minimal peak DP alignment score [80] -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n] Input/Output: -a output in the SAM format (PAF by default) -o FILE output alignments to FILE [stdout] -L write CIGAR with >65535 ops at the CG tag -R STR SAM read group line in a format like '@RG\tID:foo\tSM:bar' [] -c output CIGAR in PAF --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [none] --MD output the MD tag --eqx write =/X CIGAR operators -Y use soft clipping for supplementary alignments -t INT number of threads [3] -K NUM minibatch size for mapping [500M] --version show version number Preset: -x STR preset (always applied before other options; see minimap2.1 for details) [] - map-pb/map-ont: PacBio/Nanopore vs reference mapping - ava-pb/ava-ont: PacBio/Nanopore read overlap - asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence - splice: long-read spliced alignment - sr: genomic short-read mapping See `man ./minimap2.1' for detailed description of these and other advanced command-line options. ---------------------------------------------- Program options for samtools_view: samtools view: unrecognised option '--help' Usage: samtools view [options] || [region ...] Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to FILE [null] -t FILE FILE listing reference names and lengths (see long help) [null] -X include customized index file -L FILE only include reads overlapping this BED FILE [null] -r STR only include reads in read group STR [null] -R FILE only include reads with read group listed in FILE [null] -d STR:STR only include reads with tag STR and associated value STR [null] -D STR:FILE only include reads with tag STR and associated values listed in FILE [null] -q INT only include reads with mapping quality >= INT [0] -l STR only include reads in library STR [null] -m INT only include reads with number of CIGAR operations consuming query sequence >= INT [0] -f INT only include reads with all of the FLAGs in INT present [0] -F INT only include reads with none of the FLAGS in INT present [0] -G INT only EXCLUDE reads with all of the FLAGs in INT present [0] -s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the fraction of templates/read pairs to keep; INT part sets seed) -M use the multi-region iterator (increases the speed, removes duplicates and outputs the reads as they are ordered in the file) -x STR read tag to strip (repeatable) [null] -B collapse the backward CIGAR operation -? print long help, including note about region specification -S ignored (input format is auto-detected) --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE -T, --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --write-index Automatically index the output files [off] --verbosity INT Set level of verbosity ----------------------------------------------