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What variant callers are faster than samtools?
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4.7 years ago
usgenome2018 • 30
USA

What WGS variant callers are faster than samtools?

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

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

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How do you exactly do this?

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16 months ago
Sam ♦ 2.3k
New York

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

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thx, are there any other choices?

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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.

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17 months ago
h.mon 25k
Brazil

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).

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16 months ago
United States

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

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