
Vinod Kumar
- Total activity 25
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 2
- Subscriptions 6
Activity overview
Latest activity by Vinod Kumar-
Vinod Kumar commented,
Hi Genevieve Brandt (she/her), I couldn't find an issue why only 16 out of 973 samples failed in one particular chromosome. Just one weird thing is that files from temp directory for this particula...
-
Vinod Kumar commented,
Hi Genevieve Brandt (she/her), Thanks for the reply. Actually I am talking about that few samples failed for a particular chromosome while for rest of the chromosomes all these samples are okay. Wh...
-
Vinod Kumar created a post,
GenotypeGVCF: How can I know which sample falied in joint genotyping?
AnsweredHello, GATK versionv 4.1.9.0 I am using GenotypeGVCF for joint genotyping and it worked successfully. I had big data set generated using GenomicsDBimport. I did chromosome-wise genotyping and I did...
-
Vinod Kumar commented,
Hi Genevieve Brandt (she/her), I can't import all the chromosomes in one go so, I divided my entire analysis chromosome-wise and ran separate scripts for different chromosomes. Now, I am almost ...
-
Vinod Kumar commented,
Hi Genevieve Brandt (she/her), Thank you very much for the responses. It looks our server is overloaded now, once I'll have the results, I'll come back to you. Thanks,
-
Vinod Kumar commented,
Hi Genevieve Brandt (she/her), I repeated my analysis with --max-num-intervals-to-import-in-parallel 2 instead of 8 and the analysis stopped at same point, it only imported only 14 out of 17 batche...
-
Vinod Kumar commented,
Hi Genevieve Brandt (she/her), Actually I am working on server so overall space is not a problem. When I ran the script I had around 2TB space remaining. But still I don't know if temp directory i...
-
Vinod Kumar created a post,
GenomicsDBimport not importing all the batches
Hi, I am using GATK version 4.1.9.0. I used GenomicsDBimport to create a data store for around 850 samples with Batch size=50 (17 batches). I used the follwing script., gatk --java-options "-Xmx80g...
-
Vinod Kumar commented,
Shirely, In my case, I tried various things like you but finally I found that I had a problem in sample_map file, there was an extra '/' , I removed it and it worked for me. Error in creating Reade...
-
Vinod Kumar commented,
Ivan, I was also struggling with this but then according to suggestions from other threads, I divided the whole chromosome.interval_list into different chromosomes(1 to 8).interval_list and rerun t...