1samtools-bedcov(1)           Bioinformatics tools           samtools-bedcov(1)
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NAME

6       samtools bedcov - reports coverage over regions in a supplied BED file
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SYNOPSIS

9       samtools bedcov [options] region.bed in1.sam|in1.bam|in1.cram[...]
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DESCRIPTION

13       Reports  the  total  read  base  count  (i.e.  the sum of per base read
14       depths) for each genomic region specified in the supplied BED file. The
15       regions  are  output  as  they  appear in the BED file and are 0-based.
16       Counts for each alignment file supplied are reported in  separate  col‐
17       umns.
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OPTIONS

21       -Q, --min-MQ INT
22              Only  count  reads with mapping quality greater than or equal to
23              INT
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25       -g FLAGS
26              By default, reads that have any of the flags  UNMAP,  SECONDARY,
27              QCFAIL,  or  DUP set are skipped. To include these reads back in
28              the analysis, use this option together with the desired flag  or
29              flag  combination.   FLAGS  can be specified in hex by beginning
30              with `0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with  `0'
31              (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or
32              as a comma-separated list of flag names. [0]
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34              For a list of flag names see samtools-flags(1).
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36       -G FLAGS
37              Discard any read that has any of the flags  specified  by  FLAGS
38              set.   FLAGS  are  specified  as  for the -g option. [UNMAP,SEC‐
39              ONDARY,QCFAIL,DUP]
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41       -j     Do not include deletions (D) and ref skips (N) in bedcov  compu‐
42              tation.
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44       -d INT Print an additional column, for each file, containing the number
45              of bases having a depth above and including the given threshold.
46              If  the  option  is not used, the extra column is not displayed.
47              The option value must be an integer >= 0.
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49       -X     If this option is set, it will allows user to specify customized
50              index  file  location(s) if the data folder does not contain any
51              index file. Example usage: samtools bedcov [options] -X <in.bed>
52              </data_folder/in1.bam> [...] </index_folder/index1.bai> [...]
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AUTHOR

56       Written by Heng Li from the Sanger Institute.
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SEE ALSO

60       samtools(1)
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62       Samtools website: <http://www.htslib.org/>
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66samtools-1.15.1                  7 April 2022               samtools-bedcov(1)
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