Getinsertsize: Difference between revisions

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=Example=
=Example=
<pre>
<pre>
 
samtools view /home/thorfinn/data/victor/Merge/011557_RG.bam|head -n500000|./getinsertsize
 
Read length mean:95.677839 sqrt(var):6.814545
Read span mean:169.868832 sqrt(var):75.951989
</pre>
</pre>

Revision as of 14:33, 20 March 2014

Small ultrafast program for estimating the read length and get the insert size from uncompressed samples:

[1]

It's a faithful implementation of this script [2]

Installation

wget http://www.popgen.dk/software/download/getinsertsize.cpp
g++ getinsertsize.cpp -O3 -o getinsertsize


Example

samtools view /home/thorfinn/data/victor/Merge/011557_RG.bam|head -n500000|./getinsertsize
Read length mean:95.677839	 sqrt(var):6.814545
Read span mean:169.868832	 sqrt(var):75.951989