Program options for samtools_sort: 

samtools sort: failed to read header from "-"
sort: invalid option -- 'h'
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


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Program options for minimap2: 

Usage: minimap2 [options] <target.fa>|<target.idx> [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/splice:hq - long-read/Pacbio-CCS spliced alignment
                 - sr - genomic short-read mapping

See `man ./minimap2.1' for detailed description of these and other advanced command-line options.


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