Ubuntu Manpage: samtools-flagstat - counts the number of alignments for each FLAG type

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.
       Information on the meaning of the  flags  is  given  in  the  SAM  specification  document
       <https://samtools.github.io/hts-specs/SAMv1.pdf>.

       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:

                         primary
                                neither 0x100 nor 0x800 bit set

                         secondary
                                0x100 bit set

                         supplementary
                                0x800 bit set

                         duplicates
                                0x400 bit set

                         primary duplicates
                                0x400 bit set and neither 0x100 nor 0x800 bit set

                         mapped 0x4 bit not set

                         primary mapped
                                0x4, 0x100 and 0x800 bits 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, mapped shows 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)

The properly paired and singletons counts work in a similar way but the percentage is
against the total number of QC-passed and QC-failed pairs. The primary mapped count is a
percentage of the total number of QC-passed and QC-failed primary reads.

In the tsv and json formats, these percentages are listed in separate categories mapped %,
primary 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