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Hi
I am using sqanti3 with the following parameters :
```
Version 2.0.0
Input all_samples.chained.gff
Annotation OcoaRS1.PZYT01.fa.all.maker.functional_ipr.gff
Genome OcoaRS1.PZYT01.fa.…
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Will this ever support GATK 4.x ?
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Hi Jeremiah,
I've ran SvABA on some test BAMs and benchmarked it against other modern SV callers - it performs well, having the highest F-score on NA12878 germline sample.
Unfortunately, when I …
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`ivar` variants treats indels as any other type of variant and only uses the minimum frequency threshold to call consensus.
For example, if a position has the following bases,
```
A -> 5
AT ->…
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tdlr : Edge case where **N** being called in position where sufficient coverage in pileup for reference base pair but being missed since `nanopolish variant` called low quality variant and being filte…
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Currently, 32% of our associations in 0.8 have no genomic coordinates assigned to at least one feature.
These fall into the following categories:
- [ ] Associations harvested from CGI all lack e…
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Update Nicotine dependence meta-analysis.
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Hello,
I was able to install megSAP on our server and after a successful test run with provided panel data I am trying to run analysis of WES data. Everything runs smoothly until the VCFAnnotatefromV…
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Currently, we don't have start/end in the mapping file. This isn't a problem for 1bp-wide features like SNPs (in the strict sense of the term), but if you include indels/structural variants you can ha…
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Hi,
I'm Jia, a postdoc from UNC Charlotte. I wonder to know in the directory in the Step 2 of Mapping. Does it include all snps from all chromosomes or just heterozygous snps from all chromosomes?
…
Jia21 updated
6 years ago