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samtools-flagstat(1)	     Bioinformatics tools	  samtools-flagstat(1)

NAME
       samtools	flagstat - counts the number of	alignments for each FLAG type

SYNOPSIS
       samtools	flagstat in.sam|in.bam|in.cram

DESCRIPTION
       Does  a full pass through the input file	to calculate and print statis-
       tics to stdout.

       Provides	counts for each	of 13 categories based primarily on bit	 flags
       in  the FLAG field.  Each category in the output	is broken down into QC
       pass and	QC fail.  In the default output	format,	these are presented as
       "#PASS +	#FAIL" followed	by a description of the	category.

       The  first  row	of  output gives the total number of reads that	are QC
       pass and	fail (according	to flag	bit 0x200). For	example:

	 122 + 28 in total (QC-passed reads + QC-failed	reads)

       Which would indicate that there are a total of 150 reads	in  the	 input
       file,  122 of which are marked as QC pass and 28	of which are marked as
       "not passing quality controls"

       Following this, additional categories are given for reads which are:

			 secondary
				0x100 bit set

			 supplementary
				0x800 bit set

			 duplicates
				0x400 bit set

			 mapped	0x4 bit	not set

			 paired	in sequencing
				0x1 bit	set

			 read1	both 0x1 and 0x40 bits set

			 read2	both 0x1 and 0x80 bits set

			 properly paired
				both 0x1 and 0x2 bits set and 0x4 bit not set

			 with itself and mate mapped
				0x1 bit	set and	neither	0x4 nor	0x8 bits set

			 singletons
				both 0x1 and 0x8 bits set and bit 0x4 not set

		 And finally, two rows are given that additionally  filter  on
		 the  reference	 name (RNAME), mate reference name (MRNM), and
		 mapping quality (MAPQ)	fields:

			 with mate mapped to a different chr
				0x1 bit	set and	neither	0x4 nor	0x8  bits  set
				and MRNM not equal to RNAME

			 with mate mapped to a different chr (mapQ>=5)
				0x1  bit  set and neither 0x4 nor 0x8 bits set
				and MRNM not equal to RNAME and	MAPQ >=	5

ALTERNATIVE OUTPUT FORMATS
       The -O option can be used to select two	alternative  formats  for  the
       output.

       Using  -O  tsv selects a	tab-separated values format that can easily be
       imported	into spreadsheet software.  In this format  the	 first	column
       contains	the values for QC-passed reads,	the second column has the val-
       ues for QC-failed reads and the third contains the category names.

       Using -O	json generates an ECMA-404 JSON	data interchange format	object
       <https://www.json.org/>.	  The  top-level object	contains two named ob-
       jects QC-passed reads and QC-failed reads.  These contain  the  various
       categories listed above as names	and the	corresponding count as value.

       For  the	 default  format,  the mapped, properly	paired,	and singletons
       show the	count as a percentage of the total number of QC-passed or  QC-
       failed reads after the category name.  For example:

       32 + 0 mapped (94.12% : N/A)

       In  the	tsv and	json formats, these percentages	are listed in separate
       categories mapped %, properly paired %, and singletons %.  If the  per-
       centage	cannot	be  calculated (because	the total is zero) then	in the
       default and tsv formats it will be reported as `N/A'.  In the json for-
       mat, it will be reported	as a JSON `null' value.

OPTIONS
       -@ INT	 Set  number  of  additional  threads  to use when reading the
		 file.

       -O FORMAT Set the output	format.	  FORMAT  can  be  set	to  `default',
		 `json'	 or `tsv' to select the	default, JSON or tab-separated
		 values	output format.	If this	option is not  used,  the  de-
		 fault format will be selected.

AUTHOR
       Written by Heng Li from the Sanger Institute.

SEE ALSO
       samtools(1), samtools-idxstats(1), samtools-stats(1)

       Samtools	website: <http://www.htslib.org/>

samtools-1.11		       22 September 2020	  samtools-flagstat(1)

NAME | SYNOPSIS | DESCRIPTION | ALTERNATIVE OUTPUT FORMATS | OPTIONS | AUTHOR | SEE ALSO

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