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.

OPTIONS

       -X         This option will allow the user to specify a customised index file location. e.g.

                  samtools idxstat [options] -X /data_folder/data.bam /index_folder/index.bai

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/>

samtools-1.21                                   12 September 2024                           samtools-idxstats(1)