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/>