srubinacci
commented
4 years ago Hi Charles,
I've just re-run step1-to-5 from the scripts in the GLIMPSE/test folder and I did not encounter any problem. Can you please try to run the same scripts (adapting step1 to your environment) and see if everything runs smoothly?
Regarding bcftools, unfortunately I don't have enough information to say why you encounter the segfault, but please keep the -Ai parameter. Another problem I see here is that you might mix different genome builds/chromosome annotations. In the tutorial what we do is to download the reference panel in build38 and change the name of the chromosome from "22" to "chr22" (as usual in b38). Therefore I don't understand why you get an input region in this form: "22:47069138-50805809" instead of "chr22:47069138-50805809". The target and input files must have the same chromosome name in order to allow random access.
Hope this helps. Best wishes, Simone
cwarden45
Hi,
Thank you very much for putting together this program.
I have encountered the following issues:
1) If I run
bcftools callexactly as specified in section 3.2 of the example, then I get a segmentation fault error message from bcltools.2) If I remove the
-Aiparameters frombcftools call(and separate the command into 2 separate commands), then I no longer get a segmentation error and I can produce a valid file. However, I get an error message fromGLIMPSE_phase:While I hope to eventually update it with working code, you can see the commands that I am using here (where everything but the current step is commented out).
Have you encountered this problem before? If not, you know have any suggestions about what I might be able to try to troubleshoot this problem?
Thank you very much.
Sincerely, Charles