User: omeally

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Posts by omeally

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Comment: C: Importing VCFs in seqCAT
... Thanks Erik and James- i really appreciate how quickly you're able to help! With your explanations and a bit of googling, i found it's a bug in Mutect2 thats since been fixed (https://github.com/broadinstitute/gatk/pull/5185 ). I'll filter the haplotypecaller vcfs and try again. I'll also let the Sa ...
written 5 weeks ago by omeally0
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Comment: C: Importing VCFs in seqCAT
... Hmmm, I'm at a loss then. In the above snippt, doesn't DP=122 for that variant? ...
written 5 weeks ago by omeally0
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Comment: C: Importing VCFs in seqCAT
... Thanks for your help James, I really appreciate it! I take your point re warnings/errors (still learning R/bioconductor), but I'm confused because after running FilterMutectCalls, the filter column is populated and many variants have DP>=10, but no profile is written to disk. One eg variant: 1 ...
written 5 weeks ago by omeally0
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Comment: C: Importing VCFs in seqCAT
... Thanks for the tip, but its still not working, although the error from the mutect VCF is now similar to haplotypecaller: gatk FilterMutectCalls -V mutect2_T2_CTL_CTL_rep1_vs_T0_CTL_CTL_rep1_snpEff_VEP.ann.vcf.gz -O mutect2_T2_CTL_CTL_rep1_vs_T0_CTL_CTL_rep1_snpEff_VEP.ann.filtered.vcf.gz > vcfm&l ...
written 5 weeks ago by omeally0
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Importing VCFs in seqCAT
... I'm having some trouble importing VCFs into seqCAT. I used Sarek to produce VCFs with haplotypecaller and mutect2, and annotated with snpEff and VEP, but importing either fails: > vcf <-("../VCFs/haplotypecaller/haplotypecaller_T0_CTL_CTL_rep1_snpEff_VEP.ann.vcf.gz") > create_profile(vcf, ...
seqcat written 5 weeks ago by omeally0 • updated 5 weeks ago by erikfas30
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Comment: C: How to prepare .vcf for seqCAT
... I'm in a similar situation, but the suggestion below brings no joy. I've got germline VCFs from haplotypecaller annotated with snpEff and VEP, but they give the error: > vcf <-("../VCFs/haplotypecaller/haplotypecaller_T0_CTL_CTL_rep1_snpEff_VEP.ann.vcf.gz") > create_profile(vcf, 'T0_CTL_C ...
written 5 weeks ago by omeally0

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