Question: The genotype imputation in Beagle always stop on specific step and can not finish the imputation file
0
gravatar for r00628112
7 months ago by
r0062811210
r0062811210 wrote:

Hello~

About the genotype imputation in Beagle, I run the vcf file, but the program always stopped in this step as the attached link.(https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6)

I used this command:

java -jar beagle.25Nov19.28d.jar  gt=200212-NiNK_newPmgenomeDP5Q10maf0.2missing0.5.recode.vcf out=Imput_200212-NiNK_newPmgenomeDP5Q10maf0.2missing0.5.recode

Could anyone give me some suggestions?

Thank you very much

Screen figure

https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6

beagle genotype imputation • 317 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe65k • written 7 months ago by r0062811210
2

The window in which beagle gets stucked is only one bp long, while others are several kb. Can you give a look at the input file in the position in which beagle gets stucked? Maybe there is something strange there...

ADD REPLYlink written 7 months ago by Fabio Marroni2.6k

Sure. Thank you so much. (1) The stop site in the original VCF file: https://drive.google.com/open?id=1bHWom4I_ztD5wTMNti9bHvFwRa6eaz8Z (2)The stop site in the beagle imputation file https://drive.google.com/open?id=1RFnAY3ljjykRmibkl7cmz5z4RL-cvAXK

ADD REPLYlink modified 7 months ago • written 7 months ago by r0062811210
1

These links might help:

BEAGLE 4.1 imputation ending short with "at dag.MergeableDag" message

https://faculty.washington.edu/browning/beagle/beagle_5.0_14May18.pdf

Are there NaN's in your data?

ADD REPLYlink modified 7 months ago • written 7 months ago by Fatima610

Hi~ Thanks to your reply. I checked the vcf file, and there are no any NaN characters. Then, I followed the solution from the link (add -Xss5m), but it is no work. Thank you very much :D

ADD REPLYlink written 7 months ago by r0062811210

Which error messages are appearing? Can you reply to Fabio's comment, please?

ADD REPLYlink written 7 months ago by Kevin Blighe65k

Ok. Thank you. There are no error message, but an WARNING message showed during processing. (in this photo https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6) And the stop site information are as below: (1) The stop site in the original VCF file: https://drive.google.com/open?id=1bHWom4I_ztD5wTMNti9bHvFwRa6eaz8Z (2)The stop site in the beagle imputation file https://drive.google.com/open?id=1RFnAY3ljjykRmibkl7cmz5z4RL-cvAXK

ADD REPLYlink written 7 months ago by r0062811210
1

Mmmm, it looks like the entire chromosome contains only one SNP. Is it correct? Maybe Beagle is not ready to deal with chromosomes/regions with only one SNP. Maybe this is the issue?

BTW, it looks like the link to the warning message is broken.

ADD REPLYlink written 7 months ago by Fabio Marroni2.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1640 users visited in the last hour