Provided by: megadepth_1.2.0-4build2_amd64 
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)