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Sorry to bother you again, after using the ONT data to call the structure variation, we modified the VCF content with format_add_ALTseq_LR.R. The following error occurred, so we checked the VCF file, …
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Dear SAIGE developer,
We had run gene based SAIGE test on a small set of case control exome seq sample(137 case vs 681 controls) rare variants(MAF
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A few options (feel free to add more):
- Continue to use GATK 3.6 CombineVariants in Somatic/Multi-Caller SNV workflows
- Use GATK4 MergeVCFs (or similar) and drop the `set` annotation from any fi…
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Hello,
I am trying to run SomaticSeq on RNA data (single-end reads) but it's really slow. It never finished because I had to kill it after 7 days. I have many large samples (~10 GB) and if the smal…
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Hi,
I think people are looking for SV merge tools often, and after testing many SV merge tools, such as `SURVIVOR`, `svimmer`, `SVanalyzer`, `svtools`, `truvari`, `bcftools`, and many other tools, …
xiucz updated
8 months ago
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Chris and Sangtae;
This is a follow-up to a bcbio discussion (https://github.com/chapmanb/bcbio-nextgen/issues/2112#issuecomment-338307641) which I thought could use it's own thread. In bcbio we're c…
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Our pipeline requires that users install every variant caller at runtime, even if they don't actually use some of them.
For example, DELLY is not used by the pipeline by default, but it is still inst…
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Hi sciclone author:
1) Is there any possibility to show little more information about the header for each file (matrix).
2) Is there any possibility to show which software or R packages are fre…
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Hi,
I was wondering if it's possible to annotate both ends of a BND/TRA structural variant with vcfanno? From what I can see, it seems to annotate only one of the ends, but not the second.
For …