Wout Megchelenbrink
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Recent activity by Wout Megchelenbrink Sort by recent activity-
Hi Genevieve, The BAM files were fine, I ran the "somatic variant calling best practice" , including the AddOrReplaceReadGroups function with them. As i feared, most of the problem was caused by a...
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Hi Genevieve, I see the problem, I indeed omitted the INFO fields. Sorry, let me retry from scratch: GATK version used: 4.1.9.0 (also in 4.1.8.1) Exact command used: gatk VariantAnnotator -V s220...
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All jobs finished successfully using GATK 4.1.8.1, so the problem is solved. Best,Wout
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Dear David, Thanks for the advise. I downloaded the latest GATK version today and Mutect2 seems to run fine now. Although it did not finish the full analysis yet, it passed chr13 without problems ...