samtools depth [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]]
Computes the depth at each position or region.
Output all positions (including those with zero depth)
Output absolutely all positions, including unused reference sequences. Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file.
Compute depth at list of positions or regions in specified BED FILE. 
Use the BAM files specified in the FILE (a file of filenames, one file per line) 
Write a comment line showing column names at the beginning of the output. The names are CHROM, POS, and then the input file name for each depth column. If one of the inputs came from stdin, the name “-” will be used for the corresponding column.
Ignore reads shorter than INT. This is the number of bases in the sequence, minus any soft clips.
(Deprecated since 1.13) This option previously limited the depth to a maximum value. It is still accepted as an option, but ignored.
Note for single files, the behaviour of old samtools depth -J -q0 -d INT FILE is identical to samtools mpileup -A -Q0 -x -d INT FILE | cut -f 1,2,4
Write output to FILE. Using “-” for FILE will send the output to stdout (also the default if this option is not used).
Only count reads with base quality greater than or equal to INT
Only count reads with mapping quality greater than or equal to INT
Only report depth in specified region.
If this option is set, it will allow the user to specify customized index file location(s) if the data folder does not contain any index file. Example usage: samtools depth [options] -X /data_folder/in1.bam [/data_folder/in2.bam [...]] /index_folder/index1.bai [/index_folder/index2.bai [...]]
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. 
For a list of flag names see samtools-flags(1).
Discard reads that have any of the flags specified by FLAGS set. FLAGS are specified as for the -g option. [UNMAP,SECONDARY,QCFAIL,DUP]
Only include reads with at least one bit set in FLAGS present in the FLAG field. FLAGS are specified as for the -g option. 
Only include reads with all bits set in FLAGS present in the FLAG field. FLAGS are specified as for the -g option. 
Include reads with deletions in depth computation.
For the overlapping section of a read pair, count only the bases of the first read. Note this algorithm changed in 1.13 so the results may differ slightly to older releases.
Written by Heng Li and James Bonfield from the Sanger Institute.
Samtools website: <http://www.htslib.org/>
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