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Dear sir,
I use mutect2 to call the somatic variants and use filtermutectcalls to generate the FILTER field.
Finally, I use annovar to annotate the mutect2 output file and get three file(multianno.t…
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As discussed in issue #22 (Variant Pathogenicity Interpretation Definition and Scope), we decided that variant origin will be captured as a qualifier, and that this value should be constrained to germ…
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Hi,
I ran Strelka2 with the default parameters for WES and after running Manta:
configureStrelkaSomaticWorkflow.py \
--normalBam CM0403_1-control.md.bam \
--tumorBam CM0403_1-tumour.md.bam \
--re…
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**Is your feature request related to a problem? Please describe.**
In a validation of the GMS Lymphoid panel there's been a few variants in the reference samples that were filtered out in the VCF d…
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Hi,
I am running out of ideas as to why Strelka2 calls zero variants (no region callable?). I am doing T-N paired somatic calling on hg19 ref. using the --targeted argument.
Step1:
configureStrel…
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Hello Folks,
Strelka2 is our go to caller for standard somatic variant calling. It works well down to about 5% AF. We'd like it to work with our ctDNA variant calling where the read depth exceeds…
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Configuration file: github.toml
Description: VariantTools, software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analys…
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--Hi,
how to set Vardict to detect variants with VAF ~ 1%, which parameters can increase sensitivity ?
than you --
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Hello, I've run the somatic workflow in Strelka2 version 2.9.2 on a tumour-only-calling assay. But I get the error: "Requested indel error rates for sample index 1 when only 1 samples are defined", "F…
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Hi @fenderglass and @aysegokce , this is Khi Pin. As you know I've implemented Severus 0.1.1 in the somatic variants WDL pipeline. I've been looking into Severus 1.0 and while the majority of the trut…