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MEGADEPTH(1) User Commands MEGADEPTH(1)

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

Show this screen.
Show version.
# 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).
String to use to prefix all output files.
Force all AUC(s) to be written to <prefix>.auc.tsv rather than STDOUT
Force summarized annotation regions to be written to <prefix>.annotation.tsv rather than STDOUT
Force covered regions to be written to <prefix>.coverage.tsv rather than STDOUT
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):

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.
Only output the regions in this BED applying the argument to --op to them.
Statistic to run on the intervals provided by --annotation
Discard coordinates from output of summarized regions
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.
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)
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.

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.
Extract co-occurring jx coordinates, strand, and anchor length, per read writes to a TSV file <prefix>.jxs.tsv
Extract all jx coordinates, strand, and anchor length, per read for any jx writes to a TSV file <prefix>.all_jxs.tsv
Modifies certain buffer sizes to accommodate longer reads such as PB/Oxford.
Integer bitmask, any bits of which alignments need to have to be kept (similar to samtools view -f).
Integer bitmask, any bits of which alignments need to have to be skipped (similar to samtools view -F).
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:

Print differing from ref per-base coverages Writes to a CSV file <prefix>.alts.tsv
Print a record to the alts CSV for soft-clipped bases Writes total counts to a separate TSV file <prefix>.softclip.tsv
If --include-softclip, only print softclips which are mostly A's or T's
Print mismatch records when mismatched read base is N
Print quality values for mismatched bases
Print POS field as +/- delta from previous
Quit with error unless MD:Z field exists everywhere it's expected
Print sequence names and lengths in SAM/BAM header

Coverage and quantification:

Print per-base coverage (slow but totally worth it)
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
Output coverage as BigWig file(s). Writes to <prefix>.bw (also <prefix>.unique.bw when --min-unique-qual is specified). Requires libBigWig.
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.
Statistic to run on the intervals provided by --annotation
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.
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
Allow overlapping ends of PE read to count twice toward coverage
Report total sum of bases in alignments processed (that pass filters)
Turns on gzipping of coverage output (no effect if --bigwig is passsed), this will also enable --no-coverage-stdout.

Other outputs:

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
Print fragment length distribution across the genome Writes to a TSV file <prefix>.frags.tsv
Print a SAM record for each aligned read
Report end coordinate for each read (useful for debugging)
Lower Poly-A filter minimums for testing (only useful for debugging/testing)
July 2022 megadepth 1.2.0