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 ***@***.***> 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 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBUFZIZ6B7O5WSOTJV4ADR5WLU5ANCNFSM4PG7YKUQ> .

[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 ***@***.***> wrote: Yes, something like that will work. I use to do something like $(perl -e 'print join ",", (0..100)') — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBUFZ24GKY4VSCKKX6BTLR55AZPANCNFSM4PG7YKUQ> .

[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 ***@***.***> wrote: Thank you Zev! Will try these out. Regards. On Tue, 28 Jul 2020 at 22:41, Zev Kronenberg ***@***.***> wrote: > Yes, something like that will work. I use to do something like $(perl -e > 'print join ",", (0..100)') > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#12 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/ANJBUFZ24GKY4VSCKKX6BTLR55AZPANCNFSM4PG7YKUQ > > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAE7CIIHET4QR2472SSBPMDR6A2RXANCNFSM4PG7YKUQ> .

[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 <notifications@github.com> 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 ***@***.***> wrote: > Thank you Zev! Will try these out. > > Regards. > > On Tue, 28 Jul 2020 at 22:41, Zev Kronenberg ***@***.***> > wrote: > > > Yes, something like that will work. I use to do something like $(perl -e > > 'print join ",", (0..100)') > > > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub > > <#12 (comment)>, or > > unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/ANJBUFZ24GKY4VSCKKX6BTLR55AZPANCNFSM4PG7YKUQ > > > > . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#12 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAE7CIIHET4QR2472SSBPMDR6A2RXANCNFSM4PG7YKUQ > > . > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANJBUFYOHPNII53M3QHCBFLR6A2YLANCNFSM4PG7YKUQ> .