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 statistics 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 values 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 objects 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 percentage 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 format, 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 default 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/>