NAME

       samtools idxstats - reports alignment summary statistics

SYNOPSIS

       samtools idxstats in.sam|in.bam|in.cram

DESCRIPTION

       Retrieve and print stats in the index file corresponding to the input file.  Before calling idxstats, the
       input BAM file should be indexed by samtools index.

       If run on a SAM or CRAM file or an unindexed BAM file, this command will still produce the  same  summary
       statistics,  but  does  so  by  reading  through  the entire file.  This is far slower than using the BAM
       indices.

       The output is TAB-delimited with each line consisting of reference  sequence  name,  sequence  length,  #
       mapped  read-segments  and  # unmapped read-segments. It is written to stdout.  Note this may count reads
       multiple times if they are mapped more than once or in multiple fragments.

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-flagstat(1), samtools-index(1), samtools-stats(1)

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