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Hello!
Upon using SURVIVOR to merge 2 VCF files from the same caller, I've noticed that the `DR` field always report `0,0` despite the reads information being available in both the VCF files. What …
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The tests for vg_construct_and_index on the ABO locus example should proceed to run multi-caller workflow (2 mappers x 2 variant callers).
It needs GBWT index, which current ABOlocus/vg_construct_a…
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Hi,
We use somaticseq to just merge variants from Mutect2 and HMF Tools SAGE (the latter as "arbitrary" vcf's), the classification module is not used currently. However we were missing some multi-n…
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### Description of feature
Some users requested that Sarek produce a VCF-file which is the "intersection" of the VCF-files from the different variant-callers. Additional description can be found here…
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Hello,
I am trying to use DISCVRSeq in replacement of gatk 3.7 CombineVariants.
I use the :
java -jar ~/DISCVRSeq/DISCVRSeq-1.3.31.jar MergeVcfsAndGenotypes -R ~/hg19_UCSC_wo_hap/fasta/hg19.wo_hap…
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Hi,
We are testing xsqueezeit to compress and quickly access variant data from a large WGS cohort. The data structure concept is cool, and we liked it so far in our tests. We especially like how it…
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Howdy, thanks for your great work on GEM! I'm wondering if there's a way to get GEM to find / emit more supplementary hits with accompanying SA tag. This is important for some structural variant calle…
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We assume in a couple of places that anything stored in the av-store has been checked for validity already, yet the av-store does not guarantee this invariant. Callers ensure that by themselves, e.g. …
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I tested 2.17 to 2.24 using an inversion between two large homologous domains.
2.17 and 2.18 detection was possible using structural variant callers.
Everything after that was unable to be found.
…