Wout Megchelenbrink
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Activity overview
Latest activity by Wout Megchelenbrink-
Wout Megchelenbrink created a post,
VariantAnnotator only reports coverage and other info when there are reads on the ALT allele
GATK version used: v4.1.9.0 I have a series of WES samples and ran the somatic mutation calling pipeline (Mutect2). Next, I took the union of all the reported variants. What I would like to know is...
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Wout Megchelenbrink commented,
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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Wout Megchelenbrink commented,
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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Wout Megchelenbrink created a post,
VariantAnnotator returns NullPointerException
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.8.1 b) Exact command used: gatk VariantAnnotator -V WES.vcf.gz -I WES.bam --output WES_VA.vcf -A Coverage c) Entire ...
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Wout Megchelenbrink commented,
All jobs finished successfully using GATK 4.1.8.1, so the problem is solved. Best,Wout
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Wout Megchelenbrink commented,
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 ...
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Wout Megchelenbrink created a post,
error: read goes past end of reference
Description of the errorRunning Mutect2 (somatic mutation calling) on WES data, I get the error "read goes past end of reference" on a few samples (a minority). WES data was mapped with BWA MEM v0....