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Software update

A very hot update summary !

BWA 0.7.0

A new algorithm (BWA-MEM)  still in beta version, expected to be twice faster, and more accurate. On the short-term, it should replace BWA algorithm which apparently doesn’t handle correctly long read. I am eager to test it.

GATK 2.4

A lot of changes, first the licence, with an access to the whole source code ! As always, some accuracy and speed improvments were announced. On a first small test, I obtained a three fold time decrease for HaplotypeCaller — Nicely done, but I am still wondering whether it’ll be enough to make HaplotypeCaller practicable. A worth noticing tool appear : RegenotypeVariants, provided that you already have a rock solid set of variants, I guess the latter may give a quickly updated vcf.

Beagle 4
This is still a beta version, a big change in the input format, beagle is now working with vcf — this will simplify a lot some of my scripts–, imputation is so far not available (Coming soon ?).


This version accept ReducedRead bam from GATK 2 (I now only have one argument left for not using it). The UI changed a bit, and a direct access to genomespace is now available.


Some improvement and database updates plus the addition of snpSIFT a side software to manipulate vcf.


I was looking for a better vcf4.1 conformity, there has been some improvment (but this is still not enough to IGV’s opinion !).

Categories: emacs, Linux, NGS
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