samtools flagstat in.sam|in.bam|in.cram
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:
neither 0x100 nor 0x800 bit set
0x100 bit set
0x800 bit set
0x400 bit set
0x400 bit set and neither 0x100 nor 0x800 bit set
0x4 bit not set
0x4, 0x100 and 0x800 bits not set
0x1 bit set
both 0x1 and 0x40 bits set
both 0x1 and 0x80 bits set
both 0x1 and 0x2 bits set and 0x4 bit not set
0x1 bit set and neither 0x4 nor 0x8 bits set
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:
0x1 bit set and neither 0x4 nor 0x8 bits set and MRNM not equal to RNAME
0x1 bit set and neither 0x4 nor 0x8 bits set and MRNM not equal to RNAME and MAPQ >= 5
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.
Set number of additional threads to use when reading the file.
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.
Written by Heng Li from the Sanger Institute.
Samtools website: <http://www.htslib.org/>
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