Provided by: megadepth_1.2.0-4build2_amd64 bug

NAME

       megadepth - Quantification of genome coverage by DNA/RNA seqencing

DESCRIPTION

       megadepth 1.2.0

       BAM and BigWig utility.

   Usage:
              megadepth <bam|bw|-> [options]

OPTIONS

       -h --help
              Show this screen.

       --version
              Show version.

       --threads
              #  of  threads  to  do:  BAM decompression OR compute sums over multiple BigWigs in
              parallel if the 2nd is intended then a TXT file listing the paths to the BigWigs to
              process  in parallel should be passed in as the main input file instead of a single
              BigWig file (EXPERIMENTAL).

       --prefix
              String to use to prefix all output files.

       --no-auc-stdout
              Force all AUC(s) to be written to <prefix>.auc.tsv rather than STDOUT

       --no-annotation-stdout
              Force summarized annotation regions to be written to <prefix>.annotation.tsv rather
              than STDOUT

       --no-coverage-stdout
              Force covered regions to be written to <prefix>.coverage.tsv rather than STDOUT

       --keep-order
              Output  annotation  coverage in the order chromosomes appear in the BAM/BigWig file
              The default is to output annotation coverage in the order chromosomes appear in the
              annotation  BED  file.   This is only applicable if --annotation is used for either
              BAM or BigWig input.

       BigWig Input: Extract regions and their counts from a BigWig outputting BED  format  if  a
       BigWig file is detected as input (exclusive of the other BAM modes):

       Extracts all reads from the passed in BigWig and output as BED format.
              This  will  also  report the AUC over the annotated regions to STDOUT.  If only the
              name of the BigWig file is passed in with no other  args,  it  will  *only*  report
              total AUC to STDOUT.

       --annotation <bed>
              Only output the regions in this BED applying the argument to --op to them.

       --op <sum[default], mean, min, max>
              Statistic to run on the intervals provided by --annotation

       --sums-only
              Discard coordinates from output of summarized regions

       --distance (2200[default])
              Number of base pairs between end of last annotation and start of new to consider in
              the same BigWig query window (a form of binning) for performance.  This  determines
              the number of times the BigWig index is queried.

       --unsorted (off[default])
              There's a performance improvement *if* BED file passed to --annotation is 1) sorted
              by sort -k1,1 -k2,2n (default is to assume sorted and check for unsorted positions,
              if unsorted positions are found, will fall back to slower version)

       --bwbuffer <1GB[default]>
              Size  of  buffer for reading BigWig files, critical to use a large value (~1GB) for
              remote BigWigs.  Default setting should be fine for most uses, but  raise  if  very
              slow on a remote BigWig.

       BAM  Input:  Extract  basic  junction information from the BAM, including co-occurrence If
       only the name of the BAM file is passed in with no other args, it will *only* report total
       AUC to STDOUT.

       --fasta
              Path  to  the  reference  FASTA  file  if  a  CRAM file is passed as the input file
              (ignored otherwise) If not passed, references will be  downloaded  using  the  CRAM
              header.

       --junctions
              Extract  co-occurring jx coordinates, strand, and anchor length, per read writes to
              a TSV file <prefix>.jxs.tsv

       --all-junctions
              Extract all jx coordinates, strand, and anchor length, per read for any  jx  writes
              to a TSV file <prefix>.all_jxs.tsv

       --longreads
              Modifies certain buffer sizes to accommodate longer reads such as PB/Oxford.

       --filter-in
              Integer  bitmask,  any bits of which alignments need to have to be kept (similar to
              samtools view -f).

       --filter-out
              Integer bitmask, any bits of which alignments need to have to be  skipped  (similar
              to samtools view -F).

       --add-chr-prefix
              Adds "chr" prefix to relevant chromosomes for BAMs w/o it, pass "human" or "mouse".
              Only works for human/mouse references (default: off).

   Non-reference summaries:
       --alts Print differing from ref per-base coverages Writes to a CSV file <prefix>.alts.tsv

       --include-softclip
              Print a record to the alts CSV for soft-clipped bases  Writes  total  counts  to  a
              separate TSV file <prefix>.softclip.tsv

       --only-polya
              If --include-softclip, only print softclips which are mostly A's or T's

       --include-n
              Print mismatch records when mismatched read base is N

       --print-qual
              Print quality values for mismatched bases

       --delta
              Print POS field as +/- delta from previous

       --require-mdz
              Quit with error unless MD:Z field exists everywhere it's expected

       --head Print sequence names and lengths in SAM/BAM header

   Coverage and quantification:
       --coverage
              Print per-base coverage (slow but totally worth it)

       --auc  Print  per-base  area-under-coverage,  will  generate it for the genome and for the
              annotation if --annotation is also passed  in  Defaults  to  STDOUT,  unless  other
              params are passed in as well, then if writes to a TSV file <prefix>.auc.tsv

       --bigwig
              Output  coverage as BigWig file(s).  Writes to <prefix>.bw (also <prefix>.unique.bw
              when --min-unique-qual is specified).  Requires libBigWig.

       --annotation <BED|window_size>
              Path to BED file containing list of regions to sum  coverage  over  (tab-delimited:
              chrm,start,end). Or this can specify a contiguous region size in bp.

       --op <sum[default], mean>
              Statistic to run on the intervals provided by --annotation

       --no-index
              If using --annotation, skip the use of the BAM index (BAI) for pulling out regions.
              Setting this can be faster if doing windows across the whole genome.  This will  be
              turned on automatically if a window size is passed to --annotation.

       --min-unique-qual <int>
              Output  second  bigWig  consisting  built  only  from alignments with at least this
              mapping quality.   --bigwig  must  be  specified.   Also  produces  second  set  of
              annotation sums based on this coverage if --annotation is enabled

       --double-count
              Allow overlapping ends of PE read to count twice toward coverage

       --num-bases
              Report total sum of bases in alignments processed (that pass filters)

       --gzip Turns  on gzipping of coverage output (no effect if --bigwig is passsed), this will
              also enable --no-coverage-stdout.

   Other outputs:
       --read-ends
              Print counts of read  starts/ends,  if  --min-unique-qual  is  set  then  only  the
              alignments  that  pass  that  filter  will  be  counted here Writes to 2 TSV files:
              <prefix>.starts.tsv, <prefix>.ends.tsv

       --frag-dist
              Print fragment  length  distribution  across  the  genome  Writes  to  a  TSV  file
              <prefix>.frags.tsv

       --echo-sam
              Print a SAM record for each aligned read

       --ends Report end coordinate for each read (useful for debugging)

       --test-polya
              Lower Poly-A filter minimums for testing (only useful for debugging/testing)