1. Community
2. General Discussion
3. Lanes from same sample show very discordant called variant results.

Oh, that makes it more clear that you need Mutect2 with microbial mode. You don't need to setup any ploidy for this tool since it does not follow any germline assumptions. 

• View comment
• Gökalp Çelik
• January 18, 2025 20:24
• 0 votes

1. Community
2. Somatic
3. PlotModeledSegments: java.lang.IllegalArgumentException: Records were not strictly sorted in dictionary order.

Hi again.  Your denoised copy ratio file contains inputs from contigs that are not in the main chromosomes. All other files end up with chrY but this file goes beyond those contigs. Can you remove ...

• View comment
• Gökalp Çelik
• January 18, 2025 18:01
• 0 votes

1. Community
2. Somatic
3. Best Practices for Tumor-Only WES Data Analysis: Seeking Feedback on Variant Calling Pipeline

Hi Abhishek Ajay We recommend using the interval files from the original manufacturer for your whole exome based work.  Regards. 

• View comment
• Gökalp Çelik
• January 18, 2025 17:55
• 0 votes

1. Community
2. General Discussion
3. Lanes from same sample show very discordant called variant results.

Hi again So if this is a pooled population sequencing it is recommended that you set your ploidy according to the number of individuals included in the sample. However we do have another recommenda...

• View comment
• Gökalp Çelik
• January 18, 2025 17:53
• 0 votes

1. Community
2. Other
3. VariantToTable_ Errors in the Tab delimited output

Hi again.  The source file you pointed at did not reproduce the issue you are facing. Are you sure that you are not using another VCF file edited/created using this original source? It is possible ...

• View comment
• Gökalp Çelik
• January 18, 2025 17:49
• 0 votes

1. Community
2. New User Advice
3. Huge difference in number of mutations when switching GATK versions

Hi again. The way your workflow goes looks totally fine. As I said there are quite a bit of changes under the hood that made Mutect2 more sensitive so observing more variant calls is fine. 

• View comment
• Gökalp Çelik
• January 18, 2025 17:41
• 0 votes

1. Community
2. General Discussion
3. GenomicsDBImport ended without results

Hi Changhan Yoon It is hard to follow this log as per line log info is now merged into a single line. On the other hand it is possible that this import job was not finished successfully because I a...

• View comment
• Gökalp Çelik
• January 17, 2025 12:12
• 0 votes

1. Community
2. Other
3. VariantToTable_ Errors in the Tab delimited output

Hi Aditya Saxena Can you share some of the variant context from the original file to see if CLNSIG field is populated with string or numeric arrays? I am unable to replicate this issue so it could ...

• View comment
• Gökalp Çelik
• January 16, 2025 18:45
• 0 votes

1. Community
2. Somatic
3. PlotModeledSegments: java.lang.IllegalArgumentException: Records were not strictly sorted in dictionary order.

Hi Beetle Can you upload these files to the ftp that we provide in the article? We are unable to reach any user defined environment due to security reasons. 

• View comment
• Gökalp Çelik
• January 16, 2025 18:35
• 0 votes

1. Community
2. Germline
3. VariantFiltration ReadPosRankSum & MQRankSum undefined

I am not sure what happened to our legacy archive but this issue is simple. Short answer: You cannot have rank tests without alternate alleles so those annotations can only be calculated for sites ...

• View comment
• Gökalp Çelik
• January 16, 2025 13:25
• 0 votes