Getinsertsize
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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:
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