-
I would like to extract all merged sequences into a fasta file. I have found information on how to extract all unique sequences by using this code uniques
ToFasta(getUniques(seqtab), fout="F:/MHC_VR/…
-
I'm running a 3-ancestry tractor and I get NaN for some variants, and I've noticed its only for those variants, which have 1 or more populations with AF_ancX = 0
1) Can you explain if tractor is ac…
-
Hello,
I'm facing an issue while trying to filter indels based on minimum allele frequency. After I set the `--indel_min_af` parameter to 0.3, I can still observe indels with lower AF. I'm working…
-
Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/AGImkeller/SingleCellAlleleExperiment
Confirm the…
-
Hi,
I'm comparing the use of modkit and longphase modcall on Nanopore modified BAMs.
The modcall works well and provides a nice output format.
But I noticed that it contains only a small subset of …
-
Hi,
I would like to use UMI-tools to compute a consensus sequence from a 'read group'. Is this modification possible?
Thanks!
-
## Feature request
### Tool(s) or class(es) involved
src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java
### Description
Modification requested.
When …
-
I am trying to manually set a genotype based on Variant Allele Frequency (VAF) cutoffs.
Given the following VCF file:
```
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s…
-
Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/AGImkeller/scaeData
Confirm the following by edit…
-
**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.5/docs/FAQ.md**:
Yes.
**Describe the issue:**
I followed the [PACBIO example](https://github.com/google/deepvariant/bl…