PhaseToBlockFrequency can't find file

[HayleyMountford]

Hello,

I'm using HaploShare, and I'm getting an error message when trying to phase the haplotypes using the PhaseToBlockFrequency.exe script.

It gives the error 'Error - Unhandled exception: System.10.FileNotFoundException: Could not find file’D:\dos\HaploShare-master\HaploShare-master\allchr9_4.map'.
It always gives the error that allchr9_4.map is missing regardless of which chromosome I input, and the same error if I use a different data set.

I pressume that this file is generated by the script...?

It says that the PhaseToBlockFrequency source code is available, but I can't find where that is.
can you help?

[jonsonying]

Hi,
It seems that it is a bug. I will try to fix it. May take time because it is a project long time ago. I need to setup the testing environment.

[HayleyMountford]

To give you a bit more information, I was running build 37 build SNPs (~1.1 million SNPs) on 150 individuals, and I'd split them into chromosomes using the included perl script.

The resource files included in HaploShare are in build 36, and I couldn't find any option to use the most recent version.

Could this be contributing? Do I need to lift over to build 36 to use HaploShare, or are there updates available?

Thanks for your help... and sorry for more questions :-)

[Rosadosa]

Hi,
I have exactly the same error, has this been solved?
Also I was indeed wondering about the option to use build 37, because the GeneticDistance folder provided here also only contains chr1 as far as I can see?

I am mostly interested in finding the shared IBD blocks between multiple individuals, is this an option that could run separately with for example output from Beagle refined, which has an output in the following format:

1. First sample identifier
2. First sample haplotype index (1 or 2)
3. Second sample identifier
4. Second sample haplotype index (1 or 2)
5. Chromosome
6. Starting genomic position (inclusive)
7. Ending genomic position (inclusive)
8. LOD score (larger values indicate greater evidence for IBD)
9. cM length of IBD segment

Thank you in advance!

Best,
Roos