text: user3555: I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's  natural to expect a straightforward way of conversion between them. Sadly I have yet to find one. Vcf-kit allows for conversion between vcf file and fasta alignment, but the fasta alignment contains only the SNPs. I need the whole alignment.  Does samtools/bcftools provide option for such conversion? If not, is there any other tool?
  
  user37: I am not sure what you mean by "fasta alignment file". If you mean a multi-sequence alignment (MSA) in the fasta format, you can't get that because SAM keeps pairwise alignments only and doesn't align inserted sequences. Even if you don't care about inserted sequences, a MSA in fasta is far to big to be practical. Alternatively, by "fasta alignment file", you could mean pairwise alignment, but it is still impractical to output every pairwise alignment in a separate fasta file.
  There are tools to convert SAM to BLAST-like format if that is what you want. The following shows one of them. I believe there are other tools easier to use, but I forget what are they.
  Anyway, to install:
  wget https://raw.githubusercontent.com/lh3/minimap2/master/misc/paftools.js
  curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
  cp k8-0.2.4/k8-`uname -s` k8
  
  Then you can convert your ALN.sam with:
  ./k8 paftools.js sam2paf -L ALN.sam | ./k8 paftools.js view -l0 - | less -S
  
  Or generate a SAM stream from ALN.bam and pipe it with:
  samtools view -h ALN.bam | ./k8 paftools.js sam2paf -L - | ./k8 paftools.js view -l0 -
  
  Here is an example output:
  >MT_orang   16499   0   16025   +   MT_human    16569   576 16569   13773   16095   60  tp:A:P  mm:i:2150   gn:i:172    go:i:101
  Ref+:        577 GTTTATGTAGCTTACCTCCT---CAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCA
                   ||||||||||||||  | ||   ||||||||| |||||||||||| | ||||||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||  |||||||| || ||||| || ||||   ||  || |||| |||||||||
  Qry+:          1 GTTTATGTAGCTTA--TTCTATCCAAAGCAATGCACTGAAAATGTCTCGACGGGCCCACA-CGCCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTGAGGTTACACATGCAAGCATCCCCGCCCCAGTGAG-TCGCCCTCCAAGTCACTCTGACTAAGAGGAGCAAGCATCA
  //
  
  You can change -l0 to -l80 to print alignments in multiple lines.
  
original_text: 3555: <p>I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's  natural to expect a straightforward way of conversion between them. Sadly I have yet to find one. Vcf-kit allows for conversion between vcf file and fasta alignment, but the fasta alignment contains only the SNPs. I need the whole alignment.  Does samtools/bcftools provide option for such conversion? If not, is there any other tool?</p>
   37: <p>I am not sure what you mean by "fasta alignment file". If you mean a multi-sequence alignment (MSA) in the fasta format, you can't get that because SAM keeps pairwise alignments only and doesn't align inserted sequences. Even if you don't care about inserted sequences, a MSA in fasta is far to big to be practical. Alternatively, by "fasta alignment file", you could mean pairwise alignment, but it is still impractical to output every pairwise alignment in a separate fasta file.</p>
  
  <p>There are tools to convert SAM to BLAST-like format if that is what you want. The following shows one of them. I believe there are other tools easier to use, but I forget what are they.</p>
  
  <p>Anyway, to install:</p>
  
  <pre class="lang-bash prettyprint-override"><code>wget https://raw.githubusercontent.com/lh3/minimap2/master/misc/paftools.js
  curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
  cp k8-0.2.4/k8-`uname -s` k8
  </code></pre>
  
  <p>Then you can convert your <code>ALN.sam</code> with:</p>
  
  <pre class="lang-bash prettyprint-override"><code>./k8 paftools.js sam2paf -L ALN.sam | ./k8 paftools.js view -l0 - | less -S
  </code></pre>
  
  <p>Or generate a SAM stream from <code>ALN.bam</code> and pipe it with:</p>
  
  <pre class="lang-bash prettyprint-override"><code>samtools view -h ALN.bam | ./k8 paftools.js sam2paf -L - | ./k8 paftools.js view -l0 -
  </code></pre>
  
  <p>Here is an example output:</p>
  
  <pre><code>&gt;MT_orang   16499   0   16025   +   MT_human    16569   576 16569   13773   16095   60  tp:A:P  mm:i:2150   gn:i:172    go:i:101
  Ref+:        577 GTTTATGTAGCTTACCTCCT---CAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCA
                   ||||||||||||||  | ||   ||||||||| |||||||||||| | ||||||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||  |||||||| || ||||| || ||||   ||  || |||| |||||||||
  Qry+:          1 GTTTATGTAGCTTA--TTCTATCCAAAGCAATGCACTGAAAATGTCTCGACGGGCCCACA-CGCCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTGAGGTTACACATGCAAGCATCCCCGCCCCAGTGAG-TCGCCCTCCAAGTCACTCTGACTAAGAGGAGCAAGCATCA
  //
  </code></pre>
  
  <p>You can change <code>-l0</code> to <code>-l80</code> to print alignments in multiple lines.</p>
  