1. Community
2. Germline
3. Germline CNV calling for bulk WGS data aligned to hs37d5_PhiX.fa

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...

• View comment
• Gökalp Çelik
• April 16, 2025 05:38
• 0 votes

1. Community
2. General Discussion
3. FIX to VariantRecalibrator RScript compatibility issues with latest library scales

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...

• View comment
• Gökalp Çelik
• April 12, 2025 10:14
• 0 votes

1. Community
2. Special GATK Use Cases
3. Funcotator: htsjdk.samtools.SAMException: Query asks for data past end of contig.

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 We used to have a FTP link for toy data upload however it is no longer valid.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. 

• View comment
• Gökalp Çelik
• April 12, 2025 08:51
• Edited
• 0 votes

1. Community
2. Special GATK Use Cases
3. Funcotator: htsjdk.samtools.SAMException: Query asks for data past end of contig.

Unfortunately we need data to diagnose the problem. 

• View comment
• Gökalp Çelik
• April 09, 2025 08:26
• 0 votes

1. Community
2. Special GATK Use Cases
3. Funcotator: htsjdk.samtools.SAMException: Query asks for data past end of contig.

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 "...

• View comment
• Gökalp Çelik
• April 08, 2025 05:32
• 0 votes

1. Community
2. General Discussion
3. How to Handle Huge Differences in Sequencing Depth Between Public and In-House Data in Joint Genotyping and Downstream Population Genetics Analysis?

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 ...

• View comment
• Gökalp Çelik
• April 06, 2025 08:06
• 0 votes

1. Community
2. Special GATK Use Cases
3. java.lang.ArrayIndexOutOfBoundsException: Index 6 out of bounds for length 6

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...

• View comment
• Gökalp Çelik
• April 05, 2025 10:06
• 0 votes

1. Community
2. Special GATK Use Cases
3. java.lang.ArrayIndexOutOfBoundsException: Index 6 out of bounds for length 6

Hi cqin How did you generate those gvcf files? Can you provide details on variant calling step?

• View comment
• Gökalp Çelik
• April 05, 2025 09:07
• 0 votes

1. Community
2. Special GATK Use Cases
3. Funcotator: htsjdk.samtools.SAMException: Query asks for data past end of contig.

Can you try with chr7 instead?

• View comment
• Gökalp Çelik
• April 04, 2025 12:24
• 0 votes

1. Community
2. Non-Human
3. Where can I find the files for the GATK-microbe best practices?

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. 

• View comment
• Gökalp Çelik
• April 03, 2025 11:13
• 0 votes