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<body>
<div class="document" id="maf-convert">
<h1 class="title">maf-convert</h1>

<p>This script reads alignments in <a class="reference external" href="http://genome.ucsc.edu/FAQ/FAQformat.html#format5">maf</a> format, and writes them in
another format.  It can write them in these formats: <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/axt.html">axt</a>, blast,
blasttab, <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/chain.html">chain</a>, html, <a class="reference external" href="https://genome.ucsc.edu/FAQ/FAQformat.html#format2">psl</a>, sam, tab.  You can use it like this:</p>
<pre class="literal-block">
maf-convert psl my-alignments.maf &gt; my-alignments.psl
</pre>
<p>It's often convenient to pipe in the input, like this:</p>
<pre class="literal-block">
... | maf-convert psl &gt; my-alignments.psl
</pre>
<p>This script takes the first (topmost) maf sequence as the &quot;reference&quot;
/ &quot;subject&quot; / &quot;target&quot;, and the second sequence as the &quot;query&quot;.</p>
<p>For html: if the input includes probability lines starting with 'p',
then the output will be coloured by column probability.  (To get lines
starting with 'p', run lastal with option -j set to 4 or higher.)</p>
<div class="section" id="options">
<h2>Options</h2>
<blockquote>
<table class="docutils option-list" frame="void" rules="none">
<col class="option" />
<col class="description" />
<tbody valign="top">
<tr><td class="option-group">
<kbd><span class="option">-h</span>, <span class="option">--help</span></kbd></td>
<td>Print a help message and exit.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-p</span>, <span class="option">--protein</span></kbd></td>
<td>Specify that the alignments are of proteins, rather than
nucleotides.  This affects psl format only (the first 4
columns).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-j <var>N</var></span>, <span class="option">--join=<var>N</var></span></kbd></td>
<td>Join neighboring alignments if they are co-linear and
separated by at most N letters.  This affects psl format
only.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-n</span>, <span class="option">--noheader</span></kbd></td>
<td>Omit any header lines from the output.  This may be useful if
you concatenate outputs, e.g. from parallel jobs.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-d</span>, <span class="option">--dictionary</span></kbd></td>
<td>Include a dictionary of sequence lengths in the sam header
section (lines starting with &#64;SQ).  This requires reading the
input twice, so it must be a real file (not a pipe).  This
affects sam format only.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-f <var>DICTFILE</var></span>, <span class="option">--dictfile=<var>DICTFILE</var></span></kbd></td>
<td>Get a sequence dictionary from DICTFILE.  This affects sam
format only.  You can create a dict file using
CreateSequenceDictionary (<a class="reference external" href="http://picard.sourceforge.net/">http://picard.sourceforge.net/</a>).</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-r <var>READGROUP</var></span>, <span class="option">--readgroup=<var>READGROUP</var></span></kbd></td>
<td>Specify read group information.  This affects sam format
only.  Example: -r 'ID:1 PL:ILLUMINA SM:mysample'</td></tr>
<tr><td class="option-group">
<kbd><span class="option">-l <var>CHARS</var></span>, <span class="option">--linesize=<var>CHARS</var></span></kbd></td>
<td>Write CHARS characters per line.  This affects blast and html
formats only.</td></tr>
</tbody>
</table>
</blockquote>
</div>
<div class="section" id="hints-for-sam-bam">
<h2>Hints for sam/bam</h2>
<ul>
<li><p class="first">To run fast on multiple CPUs, and get a correct header at the top,
this may be the least-awkward way.  First, make a header (perhaps by
using CreateSequenceDictionary).  Then, concatenate the output of a
command like this:</p>
<pre class="literal-block">
parallel-fastq &quot;... | maf-convert -n sam&quot; &lt; q.fastq
</pre>
</li>
<li><p class="first">Here is yet another way to get a sequence dictionary, using samtools
(<a class="reference external" href="http://samtools.sourceforge.net/">http://samtools.sourceforge.net/</a>).  Assume the reference sequences
are in ref.fa.  These commands convert x.sam to y.bam while adding a
sequence dictionary:</p>
<pre class="literal-block">
samtools faidx ref.fa
samtools view -bt ref.fa.fai x.sam &gt; y.bam
</pre>
</li>
<li><p class="first">If a query name ends in &quot;/1&quot; or &quot;/2&quot;, maf-convert interprets it as a
paired sequence.  (This affects sam format only.)  However, it does
not calculate all of the sam pairing information (because it's hard
and better done by specialized sam manipulators).</p>
<p>Fix the pair information in y.sam, putting the output in z.bam.
Using picard:</p>
<pre class="literal-block">
java -jar FixMateInformation.jar I=y.sam O=z.bam VALIDATION_STRINGENCY=SILENT
</pre>
<p>Alternatively, using samtools:</p>
<pre class="literal-block">
samtools sort -n y.bam ysorted
samtools fixmate ysorted.bam z.bam
</pre>
</li>
</ul>
</div>
<div class="section" id="bugs">
<h2>&quot;Bugs&quot;</h2>
<ul>
<li><p class="first">For sam: the QUAL field (column 11) is simply copied from the maf q
line.  The QUAL is supposed to be encoded as ASCII(phred+33),
whereas maf q lines are encoded differently according to the UCSC
Genome FAQ.  However, if you run lastal with option -Q1, the maf q
lines will in fact be ASCII(phred+33).</p>
</li>
<li><p class="first">The blast format is merely blast-like: it is not identical to NCBI
BLAST.</p>
</li>
</ul>
</div>
</div>
</body>
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