1. Community
2. Somatic
3. GATK 4.3.0.0 Mutect2 fail to call variant

Hi, David, thank you for your reply and advice! Well, I haven't figure out what exactly cause 16507G missing. Because the other variants are called correctly and none of them is missing. I guess ma...

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• yangjw
• March 07, 2023 01:40
• Edited
• 1 vote

1. Community
2. Somatic
3. Asking for advice on Mutect2 calling in somatic but amplicon data

Hi, David, thank you for your reply. I set the '--downsampling-stride 50'  and get the ideal result. Your advice helps me a lot! Thank you again!  

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• yangjw
• February 16, 2023 08:10
• 1 vote

1. Community
2. Somatic
3. FilterMutectCalls 'haplotype' filter value assigned to variants with different PGT tag

Hi Genevieve， I have met the same problem when I used GATK 4.3.0.0 Mutect2. Here is an example. I haven't use FilterMutectCalls, but I don't know how to deal with such variants. Some of them seems ...

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• yangjw
• February 08, 2023 06:01
• 0 votes