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FreeBayes Variant Calling Runtime

Yesterday I started running the FreeBayes variant calling program on 6 whole exome sequences (each 2-3 GB) under BioLinux 8. Since it is population data, variants are being called between call of them and the reference simultaneously. The computer has 23 GB of RAM and each processor is over 2 GHZ, although the program is not running in parallel. About how long should I expect the program to take to run?

freebayes variant calling exome
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written by vhf_to_uhf • vhf_to_uhf

It will take a while. Hours perhaps a day(s) or more.

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written by GenoMax GenoMax

I figured as much, but do you have any idea how many days? How long has it taken for you to run a variant caller? I don't care so much if the example you give isn't directly applicable as an estimate for this case, I would just like to have some intuition.

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written by vhf_to_uhf • vhf_to_uhf

Last time I ran freeBayes it took about 26 hours per sample file. That was whole genome data though (for a cat).

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written by GenoMax GenoMax

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