Issues running pFST

[uod12345]

Hi Zev, I'm trying to run pFST using your GPAT++ tool. It mentions using a comma separated list of inidividuals corresponding to the VCF file. I have more than 6000 individuals in mine. Is there a shorter way to do so? Something like {0:6000}? Do let me know.

[zeeev]

Hi @uod12345,

At this time there isn't a way shorthand way to do it. You'll probably hit a character limit on the command line.

If you're comfortable with cpp, I'd suggest changing this function:

https://github.com/vcflib/vcflib/blob/master/src/pFst.cpp#L58

[uod12345]

Hi Zev,

I'm sorry, I'm not familiar with cpp; do I change it this way:

void loadIndices(map<int, int> & index, string set) > void loadIndices(map< 1, 6000> & index, string set) ? # Include the numbers instead of int?

Also, I came across a blog post which gives a solution in this link :

https://www.biostars.org/p/305937/

I have not tried it yet. Do you think this will work?

Thank you for your reply.

Regards.

On Mon, 27 Jul 2020 at 16:22, Zev Kronenberg [email protected] wrote:

Hi @uod12345 https://github.com/uod12345,

At this time there isn't a way shorthand way to do it. You'll probably hit a character limit on the command line.

If you're comfortable with cpp, I'd suggest changing this function:

https://github.com/vcflib/vcflib/blob/master/src/pFst.cpp#L58

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[zeeev]

Yes, something like that will work. I use to do something like $(perl -e 'print join ",", (0..100)')

[uod12345]

Thank you Zev! Will try these out.

Regards.

On Tue, 28 Jul 2020 at 22:41, Zev Kronenberg [email protected] wrote:

Yes, something like that will work. I use to do something like $(perl -e 'print join ",", (0..100)')

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[zeeev]

Chances are you'll max out the binomial with 6000+ samples. Consider downsampling or using wcFst.

On Wed, Jul 29, 2020 at 9:00 AM uod12345 [email protected] wrote:

Thank you Zev! Will try these out.

Regards.

On Tue, 28 Jul 2020 at 22:41, Zev Kronenberg [email protected] wrote:

Yes, something like that will work. I use to do something like $(perl -e 'print join ",", (0..100)')

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[uod12345]

I have used wcFST to calculate FST on vcftools/plink. I wanted to use GPAT++ to calculate P-values for those. I'm not sure of the effects of downsampling. Will give it a shot.

On Wed, 29 Jul 2020 at 16:02, Zev Kronenberg [email protected] wrote:

Chances are you'll max out the binomial with 6000+ samples. Consider downsampling or using wcFst.

On Wed, Jul 29, 2020 at 9:00 AM uod12345 [email protected] wrote:

Thank you Zev! Will try these out.

Regards.

On Tue, 28 Jul 2020 at 22:41, Zev Kronenberg [email protected] wrote:

Yes, something like that will work. I use to do something like $(perl -e 'print join ",", (0..100)')

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