Gökalp Çelik
- Total activity 1790
- Last activity
- Member since
- Following 0 users
- Followed by 2 users
- Votes 0
- Subscriptions 622
Activity overview
Latest activity by Gökalp Çelik-
Gökalp Çelik commented,
Hi Urja Parekh Below is an example contig ploidy priors file that you can try with your samples. CONTIG_NAME PLOIDY_PRIOR_0 PLOIDY_PRIOR_1 PLOIDY_PRIOR_2 PLOIDY_PRIOR_31 0.01 0.01...
-
Gökalp Çelik commented,
Hi Eva König plot_Tranches.R file is not part of what is produced with the RSCRIPT_FILE parameter. It is included within the resource folder of the JAR as well as our github repository. https://gi...
-
Gökalp Çelik commented,
Hi again. You may have to share data using your own resources such as google drive etc.. We used to have a FTP link for toy data upload however it is no longer valid. Regards.
-
Gökalp Çelik commented,
Unfortunately we need data to diagnose the problem.
-
Gökalp Çelik commented,
Hi Nishanth Narayan I meant using chr7:77645372-79083983 as the interval. If contig names do not match what is inside the VCF you will not get any results. Looks like your contig names start with "...
-
Gökalp Çelik commented,
Hi TJN You will certainly need imputation performed using both datasets which we may not be able to support directly using any GATK tools. You may better check ShapeIT, Beagle and some other tools ...
-
Gökalp Çelik commented,
Hi cqin Looks like you are not using GATK HaplotypeCaller for making calls before joint genotyping. We are aware that there are 3rd party commercial tools claiming compatibility with GATK however w...
-
Gökalp Çelik commented,
Hi cqin How did you generate those gvcf files? Can you provide details on variant calling step?
-
Gökalp Çelik commented,
Can you try with chr7 instead?
-
Gökalp Çelik commented,
Hi Antonio Aleman gs:// schema requires google cloud utils for command line to download. You may need to check google cloud utils for your operating system to download these files. Regards.