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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. OPTIONS -X This option will allow the user to specify a customised in- dex file location. e.g. samtools idxstat [options] -X /data_folder/data.bam /in- dex_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)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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