Getinsertsize

NB newest version is on ANGSD github

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]

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