NAME

megadepth - Quantification of genome coverage by DNA/RNA seqencing

DESCRIPTION

megadepth 1.2.0

BAM and BigWig utility.

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).