text: user1770: I subset a BAM to only include primary reads using the following samtools commands:
  samtools view -F 256 input.bam > input.primaryOnly.sam
  
  Now, in order to convert this SAM into a new subsetted BAM, I would need to add a header. The way I normally do this is with Picard:
  java -jar picard.jar ReplaceSamHeader \
        I=input.primaryOnly.sam \
        HEADER=input.header.sam \
        O=new.sam
  
  whereby the header input.header.sam is from the original BAM: 
  samtools view -H input.bam > input.header.sam
  
  Then I could convert the SAM into a BAM with 
  samtools view -S -b i new.sam > new.bam
  
  My problem is, I'm using the original BAM header. If I look back at the BAM, it now contains wrong information, e.g.
  samtools flagstat new.bam
  
  might save that secondary alignments exist, when they don't. 
  How do I get a BAM header that makes sense given my new BAM (with only primary alignments)? 
  
  user73: Your first command only needs a slight modification to add in -h. This will create a SAM file with a header.
  samtools view -h -F 256 input.bam > headered.input.primaryOnly.sam
  
  
  -h        Include the header in the output.
  
  If your primary end goal is to create a BAM, then as Pierre has pointed out you can create BAM files directly from samtools view with the -b option:
  samtools view -b -F 256 input.bam > input.primaryOnly.bam
  
  And if your end-goal is a sorted BAM file, then pipe the BAM output through samtools sort:
  samtools view -b -F 256 input.bam | samtools sort > sorted.input.primaryOnly.bam
  
  
  So that's fixing what I think your problem is, but what about the specific question that you have asked, i.e. how can a header be added to an existing headerless SAM file?
  If you have an existing BAM file, you can use Picard (as you have mentioned), or manually piece the files together with cat, which will have a similar function (although Picard probably includes a few checks to make sure that the header is consistent with the input file):
  (samtools view -H input.bam; cat input.primaryOnly.sam) > headered.input.primaryOnly.sam
  
  If the only thing that matters is that the BAM file has correct reference information (which is fairly common), then the -T option can be used with samtools view. Again, -h or -b is required to make sure both the header and the usual SAM fields are displayed:
  samtools view -T reference.fa -h input.primaryOnly.sam > headered.input.primaryOnly.sam
  samtools view -T reference.fa -b input.primaryOnly.sam > headered.input.primaryOnly.bam
  
  
original_text: 1770: <p>I subset a BAM to only include primary reads using the following samtools commands:</p>
  
  <pre><code>samtools view -F 256 input.bam &gt; input.primaryOnly.sam
  </code></pre>
  
  <p>Now, in order to convert this SAM into a new subsetted BAM, I would need to add a header. The way I normally do this is with Picard:</p>
  
  <pre><code>java -jar picard.jar ReplaceSamHeader \
        I=input.primaryOnly.sam \
        HEADER=input.header.sam \
        O=new.sam
  </code></pre>
  
  <p>whereby the header <code>input.header.sam</code> is from the original BAM: </p>
  
  <pre><code>samtools view -H input.bam &gt; input.header.sam
  </code></pre>
  
  <p>Then I could convert the SAM into a BAM with </p>
  
  <pre><code>samtools view -S -b i new.sam &gt; new.bam
  </code></pre>
  
  <p>My problem is, I'm using the original BAM header. If I look back at the BAM, it now contains wrong information, e.g.</p>
  
  <pre><code>samtools flagstat new.bam
  </code></pre>
  
  <p>might save that secondary alignments exist, when they don't. </p>
  
  <p>How do I get a BAM header that makes sense given my new BAM (with only primary alignments)? </p>
   73: <p>Your first command only needs a slight modification to add in <code>-h</code>. This will create a SAM file with a header.</p>
  
  <pre><code>samtools view -h -F 256 input.bam &gt; headered.input.primaryOnly.sam
  </code></pre>
  
  <blockquote>
    <p><strong>-h</strong>        Include the header in the output.</p>
  </blockquote>
  
  <p>If your primary end goal is to create a BAM, then as Pierre has pointed out you can create BAM files directly from <code>samtools view</code> with the <code>-b</code> option:</p>
  
  <pre><code>samtools view -b -F 256 input.bam &gt; input.primaryOnly.bam
  </code></pre>
  
  <p>And if your end-goal is a <em>sorted</em> BAM file, then pipe the BAM output through samtools sort:</p>
  
  <pre><code>samtools view -b -F 256 input.bam | samtools sort &gt; sorted.input.primaryOnly.bam
  </code></pre>
  
  <hr>
  
  <p>So that's fixing what <em>I</em> think your problem is, but what about the specific question that you have asked, i.e. how can a header be added to an existing headerless SAM file?</p>
  
  <p>If you have an existing BAM file, you can use Picard (as you have mentioned), or manually piece the files together with <code>cat</code>, which will have a similar function (although Picard probably includes a few checks to make sure that the header is consistent with the input file):</p>
  
  <pre><code>(samtools view -H input.bam; cat input.primaryOnly.sam) &gt; headered.input.primaryOnly.sam
  </code></pre>
  
  <p>If the only thing that matters is that the BAM file has correct reference information (which is fairly common), then the <code>-T</code> option can be used with <code>samtools view</code>. Again, <code>-h</code> or <code>-b</code> is required to make sure both the header and the usual SAM fields are displayed:</p>
  
  <pre><code>samtools view -T reference.fa -h input.primaryOnly.sam &gt; headered.input.primaryOnly.sam
  samtools view -T reference.fa -b input.primaryOnly.sam &gt; headered.input.primaryOnly.bam
  </code></pre>
  