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

6       samtools idxstats - reports alignment summary statistics
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SYNOPSIS

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

13       Retrieve  and  print stats in the index file corresponding to the input
14       file.  Before calling idxstats, the input BAM file should be indexed by
15       samtools index.
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17       If  run  on  a  SAM or CRAM file or an unindexed BAM file, this command
18       will still produce the same summary statistics, but does so by  reading
19       through  the  entire  file.   This is far slower than using the BAM in‐
20       dices.
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22       The output is TAB-delimited with each line consisting of reference  se‐
23       quence  name,  sequence  length,  # mapped read-segments and # unmapped
24       read-segments. It is written to stdout.  Note this may count reads mul‐
25       tiple times if they are mapped more than once or in multiple fragments.
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AUTHOR

29       Written by Heng Li from the Sanger Institute.
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SEE ALSO

33       samtools(1), samtools-flagstat(1), samtools-index(1), samtools-stats(1)
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35       Samtools website: <http://www.htslib.org/>
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39samtools-1.13                     7 July 2021             samtools-idxstats(1)