-
BWA-MEM 0.7.4 does not output single-end mapping qualities. Running bam-readcount results in millions (one per read) of warnings. Please emit one warning and suppress all following warnings.
```
Coul…
-
The current VCF specification does a very admirable job of defining the standards by which variant callers should report genotypes (GT), genotype likelihoods (GL), and overall observed depth (DP) for …
arq5x updated
9 years ago
-
Hi Brad,
When I was using both svcaller: cnvkit and ensemble (>=2) for
variantcaller:
- mutect
- freebayes
- vardict
- varscan
on tumor-normal exome-seq analysis and found the followin…
-
I installed gemini by doing:
bcbio_nextgen.py upgrade --tools --toolplus data
but when running ./run_test2 speed=2, I got the following error:
[2014-05-31 09:13] Gemini cannot open this annotation f…
-
The LOH command is not working for me, it doesn't seem to like my VarScan VCF file. Any ideas?
Thanks
```
cnvkit.py scatter Sample.cnr -s Sample.cns -v VarScan.snp.Germline.vcf
Traceback (most recen…
-
Hi,
I'd like to use vt partition to identify the similarities and differences between variants called by different variant callers on the same set of samples.
However I'm having some issues...
- usi…
-
Masking in the read-mapping stage only results in removing reads that are only in the masked regions. It does not remove reads that are overlapping but that are anchored in the unmasked regions. The…
-
The first test of somatic-variation hit an error after about 1 min. The top of the error log looks like this:
```
2013-11-27 16:41:10-0600 clia1: Executing detect variants step
2013-11-27 16:41:14-0…
-
It looks like one of the runs produced non-functional GEMINI files:
```
gemini interactions Sample_174-varscan.db
Traceback (most recent call last):
File "/usr/bin/gemini", line 5, in
pkg_res…
-
Hi Brad/Rory,
Running med-high coverage (~150x) tumor/normal exome calling with multiple callers (varscan, freebayes, + trying vardict for the 1st time) -- it looks like vardict is moving _much_ slow…