Need earlier version of fastPHASE

Question

[Gennady Khvorykh]

Does anybody have fastPHASE 1.4? The current one is fastPHASE 1.4.8 (May 24th, 2013).

[h.mon]

Maybe you will have better luck contacting the authors. But why do you need an older version?

[Gennady Khvorykh]

The older version contains functionality that is absent in the current version. It is a procedure to select the optimal number of haplotype clusters (K). The parameter is used in statistical model utilized in fastPHASE. I write the wrapper script for the current version of the program that reproduces the K selection procedure. The idea is to compare the results obtained with the custom script and older version of the program.

[benjamin.pelissie]

Hi Gennady. I am very interested in using your script. Would you be willing to share it (along with instructions)? Ben

[benjamin.pelissie]

Thanks Gennady! I will look into it :)

Answer 1

[Gennady Khvorykh]

Hi Ben! Catch a link to the script. Questions, comments and suggestions are quite welcome!

Answer 2

[benjamin.pelissie]

Gennady, I get an error:

pelissie@denali:/data2/CPBWGS/Programs/kselection-master$ ./make_test_files.R -o /data2/CPBWGS/WORKING_DIR/Analyses/hapFLK/3rd_round/k_values_comparisons/custom_script/chr1 /data2/CPBWGS/WORKING_DIR/Analyses/hapFLK/3rd_round/k_values_comparisons/custom_script/plink2fastphase_chr1.recode.phase.inp
0 sequences and NA markers are loaded from /data2/CPBWGS/WORKING_DIR/Analyses/hapFLK/3rd_round/k_values_comparisons/custom_script/plink2fastphase_chr1.recode.phase.inp.
Counting missing genotypes...
Error in seq.default(2, length(mindex), 2) : wrong sign in 'by' argument
Calls: main ... GetMissing -> GetMissingMarkers -> seq -> seq.default
Execution halted
pelissie@denali:/data2/CPBWGS/Programs/kselection-master$

Do you know what's going on?

Answer 3

[Gennady Khvorykh]

It looks like input file plink2fastphase_chr1.recode.phase.inp wasn't parsed by the script. Could you send me the file or 10 first rows of it? I'll tune the code. Send all information to info [at] inzilico.com.

Answer 4

[benjamin.pelissie]

Thanks Gennady. I'm sending it.