text: user14102: When I tried to use samtools to split a bam file based on different chromosomes, I used this command:
  samtools view input.bam -b chr21 | chr21.bam
  
  However, I get error messages like this:
  -bash: chr21.bam: command not found
  [W::hts_idx_load3] The index file is older than the data file: input.bam.bai
  
  How could I solve this problem? Thanks in advance~~~
  The version I am using is:
  Program: samtools (Tools for alignments in the SAM format)
  Version: 1.10 (using htslib 1.10.2)
  
  
  user104: Try re-indexing your bam file:
  samtools index input.bam
  
  Or update the timestamp via touch index.bam.bai but I think re-indexing is safer. You might want to save any original index file first, e.g. via mv input.bam.bai old_input.bam.bai or similar
  Also I think you meant > chr21.bam instead of piping via | chr21.bam if you want to save the output file
  
original_text: 14102: <p>When I tried to use samtools to split a bam file based on different chromosomes, I used this command:</p>
  <pre><code>samtools view input.bam -b chr21 | chr21.bam
  </code></pre>
  <p>However, I get error messages like this:</p>
  <pre><code>-bash: chr21.bam: command not found
  [W::hts_idx_load3] The index file is older than the data file: input.bam.bai
  </code></pre>
  <p>How could I solve this problem? Thanks in advance~~~</p>
  <p>The version I am using is:</p>
  <pre><code>Program: samtools (Tools for alignments in the SAM format)
  Version: 1.10 (using htslib 1.10.2)
  </code></pre>
   104: <p>Try re-indexing your bam file:</p>
  <pre><code>samtools index input.bam
  </code></pre>
  <p>Or update the timestamp via <code>touch index.bam.bai</code> but I think re-indexing is safer. You might want to save any original index file first, e.g. via <code>mv input.bam.bai old_input.bam.bai</code> or similar</p>
  <p>Also I think you meant <code>&gt; chr21.bam</code> instead of piping via <code>| chr21.bam</code> if you want to save the output file</p>
  