samtools-bedcov - reports coverage over regions in a supplied BED file
samtools bedcov [
options]
region.bed
in1.sam|
in1.bam|
in1.cram[...]
Reports the total read base count (i.e. the sum of per base read depths) for
each genomic region specified in the supplied BED file. The regions are output
as they appear in the BED file and are 0-based. Counts for each alignment file
supplied are reported in separate columns.
-
-Q, --min-MQ INT
- Only count reads with mapping quality greater than or equal
to INT
-
-g FLAGS
- By default, reads that have any of the flags UNMAP,
SECONDARY, QCFAIL, or DUP set are skipped. To include these reads back in
the analysis, use this option together with the desired flag or flag
combination. FLAGS can be specified in hex by beginning with `0x'
(i.e. /^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/),
as a decimal number not beginning with '0' or as a comma-separated list of
flag names. [0]
For a list of flag names see samtools-flags(1).
-
-G FLAGS
- Discard any read that has any of the flags specified by
FLAGS set. FLAGS are specified as for the -g option.
[UNMAP,SECONDARY,QCFAIL,DUP]
- -j
- Do not include deletions (D) and ref skips (N) in bedcov
computation.
-
-d INT
- Print an additional column, for each file, containing the
number of bases having a depth above and including the given threshold. If
the option is not used, the extra column is not displayed. The option
value must be an integer >= 0.
- -c
- Print an additional column with the read count for this
region. This will be +1 for every read covering the region, not just
starting within in. The whole read filtering options -Q, -g
and -G options will also have an affect on this count, but
-d will not.
- -X
- If this option is set, it will allows user to specify
customized index file location(s) if the data folder does not contain any
index file. Example usage: samtools bedcov [options] -X <in.bed>
</data_folder/in1.bam> [...] </index_folder/index1.bai> [...]
Written by Heng Li from the Sanger Institute.
samtools(1)
Samtools website: <
http://www.htslib.org/>