1. Community
2. Special GATK Use Cases
3. CombineGVCFs

Hi Shaun Clare, We have seen this issue before with long chromosomes and creating the index for the VCF output. Another user found a workaround, which is to work with unzipped VCF files. So, try ma...

• View comment
• Genevieve Brandt (she/her)
• January 12, 2022 16:12
• 1 vote

1. Community
2. Somatic
3. Problems in subsampling reads for Mutect2 with --max-reads-per-alignment-start

Hi yqiu, Thanks for writing into the forum! I hope we can figure out what is going on with this site! I'm wondering what other troubleshooting steps you have tried in order to call this site? We ha...

• View comment
• Genevieve Brandt (she/her)
• January 06, 2022 16:27
• 1 vote

1. Community
2. Somatic
3. Mutect2 issue with --force-active: not all regions are active

Hi Maria Litovchenko, Thank you for your patience while we looked into this. I know it's not ideal to have to wait so long for answers. To find the underlying issue, we had to get the insight of ou...

• View comment
• Genevieve Brandt (she/her)
• January 05, 2022 19:46
• 1 vote

1. Community
2. General Discussion
3. HaplotypeCaller and GenotypeGVCFs

If you have more than one sample, we recommend running HaplotypeCaller in GVCF mode and then GenotypeGVCFs. This is our joint genotyping method, we have a couple resources about what that means her...

• View comment
• Genevieve Brandt (she/her)
• January 05, 2022 02:23
• 1 vote

1. Community
2. General Discussion
3. How to plot single gremlin CNV case sample against cohort mode in a figure?

Okay great! Thanks for the update Faisal.

• View comment
• Genevieve Brandt (she/her)
• December 20, 2021 17:57
• 1 vote

1. Community
2. General Discussion
3. GATK tutorial workflows

Hi Muhammad Shoaib Akhtar, These figures are are not copyright free. For any use referencing our GATK tools or documentation, please cite us following these recommendations. If it's for a presentat...

• View comment
• Genevieve Brandt (she/her)
• December 17, 2021 19:03
• 1 vote

1. Community
2. Special GATK Use Cases
3. HaplotypeCaller does not work

Hi Roohollah kheiri, Thanks for writing into the forum so we can help to get HaplotypeCaller working for you! The error message with helpful information is here: java.lang.IllegalStateException: th...

• View comment
• Genevieve Brandt (she/her)
• December 16, 2021 18:53
• 1 vote

1. Community
2. Documentation Questions
3. "NotDuplicateReadFilter" behaviour in HaplotypeCaller

Yes, that's true. It is searching for reads marked with the 0x400 flag.

• View comment
• Genevieve Brandt (she/her)
• December 08, 2021 18:13
• 1 vote

1. Community
2. Documentation Questions
3. picard sortvcf: what does it do?

Thanks Thomas, I'll look into this on my end and let you know what I find.

• View comment
• Genevieve Brandt (she/her)
• December 02, 2021 04:11
• 1 vote

1. Community
2. General Discussion
3. MergeBamAlignement error

Hi Quentin Chartreux, It looks like samtools and FastqtoSam are sorting your ubam differently which is resulting in this problem. If you create the ubam with samtools, you can run SortSam in GATK t...

• View comment
• Genevieve Brandt (she/her)
• December 01, 2021 20:29
• 1 vote