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samtools-idxstats(1)	     Bioinformatics tools	  samtools-idxstats(1)

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 in-
       dices.

       The output is TAB-delimited with	each line consisting of	reference  se-
       quence  name,  sequence	length,	 # mapped read-segments	and # unmapped
       read-segments. It is written to stdout.	Note this may count reads mul-
       tiple 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/>

samtools-1.11		       22 September 2020	  samtools-idxstats(1)

NAME | SYNOPSIS | DESCRIPTION | AUTHOR | SEE ALSO

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