Getinsertsize: Difference between revisions
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;NB newest version is on ANGSD github | |||
Small ultrafast program for estimating the read length and get the insert size from uncompressed samples: | Small ultrafast program for estimating the read length and get the insert size from uncompressed samples: | ||
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It's a faithful implementation of this script [http://allaboutbioinfo.blogspot.dk/2012/04/estimating-paired-end-read-insert.html] | It's a faithful implementation of this script [http://allaboutbioinfo.blogspot.dk/2012/04/estimating-paired-end-read-insert.html] | ||
It only uses the paired end reads that have a perfect match, and where the pair matches the same chromosome. | |||
=Installation= | =Installation= | ||
<pre> | <pre> | ||
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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> | ||
Latest revision as of 09:02, 18 September 2014
- NB newest version is on ANGSD github
Small ultrafast program for estimating the read length and get the insert size from uncompressed samples:
It's a faithful implementation of this script [2]
It only uses the paired end reads that have a perfect match, and where the pair matches the same chromosome.
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