-
added AVIA_not_found column. It seems AVIA does not have complete MAF list.
Case | Khanlab | AVIA | Both | Khanlab Only | AVIA Only | AVIA Only Not Found | Khanlab Only (%) | AVIA Only (%) | AVIA O…
-
Hello ,
I applied freebayes to my different samples, generated a VCF file, and annotated it.
I would like to know how I can determine **the frequency of each variant per sample.**
this is how my …
-
Hello!
I am running into an issue when running the pogemom.pl script (Not the Input_POGENOM pipeline, as I already had a VCF file available from bcftools). I am using the v.0.8.3 release. The comman…
-
I'm getting an [error trying to feed `Varscan2.3.9` data into `SnpEff`](https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876). The developer says this is because the `ID` column is mis…
-
- Mutect2 calling
- From a combined VCF file with two genotypes {tumor, normal}, annotate the variants with SnpEff, and output a protein XML with those variations
- Adapt `Proteomics.VariantApplicat…
-
When trying to load a VCF in IGV it gives the following error message:
```
The provided VCF file is malformed at approximately line number 69: The VCF specification does not allow for whitespace in th…
-
tb-profiler 4.4.1 has "OSError: [Errno 18] Invalid cross-device link" error. Same error has been fixed in ntm-profiler.
-
The README says "The GFF must contain the reference sequence in Fasta format"
This seems to explain why our first attempt to use SnpEffWrapper failed (snpEff build could not find the FASTA files in…
-
when i train snippy using the data offered by author,
snippy --outdir mut1 --ref example.gbk --ctgs example.fna
I have the following problem:
Error: A JNI error has occurred, please check your ins…
-
- What repositories should we have? Suggestions so far include:
- Sequence data, non-sequence-data
- One per family (sequence data), one for periodically updated data (blast DBs, kraken, snp…