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

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

58       samtools(1)
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60       Samtools website: <http://www.htslib.org/>
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64samtools-1.13                     7 July 2021               samtools-bedcov(1)
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