search

zkutalik / ssimp_software

GNU General Public License v3.0
16 stars 10 forks source link

Is it possible to manually specify the correct reference build? #106

Open jluningham opened 4 years ago

jluningham commented 4 years ago

Hi,

I am running ssimp with GWAS and REF data that were both HG19 build. I am distributing the process across chromosomes for computational speed. For some reason, ssimp detects a "tie" in counts between hg18 and hg19 when checking "count_of_hg18_1based, count_of_hg19_1based" for the reference panel, and therefore the program proceeds with a reference panel build of hg18. Because of this, a very small proportion (0.002) of GWAS SNPs are identified as tags. For all other chromosomes, the correct reference build is detected. The count of known SNPs is 7.5 million when the correct reference build is selected, but is only 194,000 in the log of this particular chromosome.

I did not see an option to specify the build in command line. I am using the compiled version because I had issues recompiling on my server, so manually adjusting the source code is not an option at this point.

Thanks for your help!

PandaPowell commented 3 years ago

Hello,

In know it has been sometime time, but was there any update to this?

I am experiencing the same problem, a tie in counts between hg18 and hg19, thus, hg18 is incorrectly picked as the build of my reference genome.

Is this a simple work around to this? I appreciate the help.

Capture