What variant callers are faster than samtools?

Question

[usgenome2018]

What WGS variant callers are faster than samtools?

It takes several hours to generate VCF file using samtools mpileup.

[Pierre Lindenbaum]

"It takes several hours to generate VCF file using samtools mpileup." : split your analysis and parallelize by chromosome

[rls_08]

How do you exactly do this?

Answer 1

[Sam]

You can try ISAAC which is from illumina. However, the VCF file generated doesn't seems to be compatible with GATK standard.

[usgenome2018]

thx, are there any other choices?

[Sam]

You can also try Platypus, but then I guess if you have sufficient computational resources, Pierre Lindenbaum's suggestion of splitting by chromosome will be the easiest way to speed things up.

Answer 2

[h.mon]

You could try BALSA or FermiKit.

You could try describing your problem in more detail to get more useful answers. And you should consider not posting several broad questions on a short period, this may lead to people ignoring your posts and / or your account being suspended.

edit: I am not a moderator and this is a suggestion based on me observing other accounts being closed by such behaviour (posting several broad questions per day).

Answer 3

[harold.smith.tarheel]

FreeBayes and VarScan2 are two additional variant callers you can try.