I'm interested in somatic variants with very low variant allele fraction. Would I miss variants have low VAF value if I use this app? I'm looking for variants have variant allele fraction ?0.02.
@Burcu Çevik? did you ever make any progress with the mutectcaller app? I like the idea of using a GPU-accelerated version, but am I right that it seems to lack some really basic functionality of mutect2 (like specifying a panel of normal or any germline resources)?
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@Patrick Maclean? You're absolutely right. If you want to use a vcf file which panel of normals as a input file, there's no such option. Mutectcaller not support Panel of Normals. Also, There is not Panel Of Normals Builder tool in tools library in UKB RAP. I created a new topic about these problems in the NVIDIA Parabricks Developer Forum 7 month ago. Nobody answered my question. Then I sent a message to UK Biobank about this topic. Unfortunately, I did not receive an answer.
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Hi @Gary Burnett?, please do you have any tips for resolving this topic?
@Burcu Çevik? did you ever make any progress with the mutectcaller app? I like the idea of using a GPU-accelerated version, but am I right that it seems to lack some really basic functionality of mutect2 (like specifying a panel of normal or any germline resources)?
@Patrick Maclean? You're absolutely right. If you want to use a vcf file which panel of normals as a input file, there's no such option. Mutectcaller not support Panel of Normals. Also, There is not Panel Of Normals Builder tool in tools library in UKB RAP. I created a new topic about these problems in the NVIDIA Parabricks Developer Forum 7 month ago. Nobody answered my question. Then I sent a message to UK Biobank about this topic. Unfortunately, I did not receive an answer.
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