-
Initial notes on proposed scope and definition of these VA type, based on requirements and considerations documented [here](https://docs.google.com/document/d/1J4AqGDEqyK8KAzfiowgHYKJNvzHuwHSHgkN9dleL…
-
I use hap.py to compare germline variants with engine=vcfeval.
I see some variants line with BD=N.
what's the meaning of "BD=N"? it's seems that variants called in both TRUTH and QUERY.
Thanks!
JY…
-
Dear @antonylebechec,
I tried to analyze a single BAM file, by the following command:
`STARK --application=GERMLINE --reads=2336.bam --analysis_name=MyFirstAnalysis --design=target_new.bed --resul…
-
### Description of the bug
I cannot finish the test of haplotypecaller tool on singularity container.
Of course, when I run my germline samples, I obtained the same error.
The pipeline fails on t…
-
As discussed in issue #22 (Variant Pathogenicity Interpretation Definition and Scope), we decided that variant origin will be captured as a qualifier, and that this value should be constrained to germ…
-
Hi,
I am trying to run a large `phase` job. 300 CRAM files with average size of between 30-40 GB per CRAM file. I also have a 42 million line VCF file of "germline variants". My LSF job terminated…
-
### Submitter Name
Grace Pendlebury
### Submitter Affiliation
Shariant / Australian Genomics
### Submitter Github Handle
_No response_
### Additional Submitter Details
Shariant is…
-
Hello,
@dlaehnemann mentioned adding varlociraptor to a benchmark we have set up in #157, and I have some questions about recommendations for setting that up.
We currently have an internal bench…
-
It should include the following:
- filter_variants (this should filter the file)
* filter_vardict: https://github.com/mskcc/ACCESS-Pipeline/blob/master/cwl_tools/basicfiltering/filter_vardict.py
…
-
In the context of somatic mutations there is no easy way to represent a genotype in the same way as in germline variants. For this reason, some somatic mutation callers, do not provide genotype inform…