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/>