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Hi, I can't pull the docker image:
docker.io/broadinstitute/pcawg_broad_wgs_variant_callers:latest
Is there some other place the image can be pulled from?
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Hello, I'm attempting to try out your tool and to start i have tried out:
```
singularity exec -e mergesvvcf_0.0.1.sif mergesvvcf -l delly,manta -o test.out -sv sample.delly.vcf.gz sample.manta.vcf.…
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I have enjoyed using Clair3 (clair3-arm64) for examining natural variants at the whole-genome level. However, I've recently noticed some irregularities that likely need correction.
Specifically, I …
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I want to compare the variant calls that I get with sinvict with other variant callers. So either I need a vcf from sinvict, or a function to convert a vcf to the sinvict format. As I've seen some pub…
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`template.HTMLEscape` and `template.JSEscape` each accept an `io.Writer` and write to it. However, they ignore errors from `Write`.
That's fine when the destination `io.Writer` is one that cannot f…
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If we have a mix of ploidies in a `.vcz` file, we create sample nodes for the maximum ploidy size for each individual, that just attach to the root (because they have no data). I.e. we make a huge pol…
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Hi,
I am using evaluate_SV_callers.pl script to compare the variants against a simulation truth VCF file which contains DEL, INS, DUP, SNP and complex variants. However, when I use this truth vcf f…
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- [ ] For each assay-type supported by Roslin, extract normal sample genotype columns from unfiltered VCFs, and merge into massive multi-sample VCFs per assay-type - listing all events observed in nor…
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The VCFs generated by QDNAseq do not conform to the specification for the reference allele field, as they contain symbolic alleles e.g. ``. This results in errors when trying to either validate the VC…
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For the Guacamole paper we'll need to compare Guacamole against mutect, strelka, and other callers if possible (e.g. mutect2) using the benchmarks in this repo. This could also potentially be a basis …