<p>Hi all.</p>

<p>I was running coverageBed with my exome bam file but it takes too long time and it hasn&#39;t returned output value.</p>

<p>Is it right that coverageBed takes much time to finish?</p>

<p>my bed file was very tiny so I thought that something might go in a wrong way.</p>

<p>below is my command and my bed file.</p>

<pre>
coverageBed -abam /DATA1/dmcb/TAR22_WES/TAR22S_sequence_readgroup_sort_dup_remove_realigned_recal.bam -b fgfr.bed -d &gt; TAR22.cov.del.b36

10   123239372       123239472</pre>

<p>You might try this:</p>

<pre>
samtools view -u -L fgfr.bed myaln.bam \
| coverageBed -abam - -b fgfr.bed -d &gt; out.bed</pre>

<p>Which means: First get the reads overlapping your bed file, then do the counting.</p>

<p>With 20GB of bam file I&#39;m not surprised coverageBed takes more then 10 min.</p>

<p>(By the way, the title of your post is misleading as there is no error reported in your question)</p>
