SkyWarrior
- Total activity 175
- Last activity
- Member since
- Following 0 users
- Followed by 4 users
- Votes 1
- Subscriptions 59
Activity overview
Latest activity by SkyWarrior-
SkyWarrior commented,
Here is the key to the problem. 17:00:13.194 WARNING gcnvkernel.io.io_commons - The saved model is created with a different version of gcnvkernel (saved: 0.7, current: 0.8). Backwards compatibility...
-
SkyWarrior commented,
Interesting. Can you run a ValidateVariants on your vcf file to see if there is anything wrong?
-
SkyWarrior commented,
Bad Address exception tells that there is a problem accessing files or maybe temporary files used by gatk. Is it possible for you to move the --tmp-dir to a directory where you have read write acce...
-
SkyWarrior commented,
This would be a matter of trial and error. It will definitely show something but may contain high numbers of false positive or false negative results compared to a PON with many more samples.
-
SkyWarrior commented,
Unless you have your targets available it will be a problem to compare against the PON using the same targets. One particular solution could be to generate these target regions using an older versi...
-
SkyWarrior commented,
This particular error was quite prominent in all of my skylake/cascade lake class hardware especially when I used openjdk provided by the OS repository. Is it possible for you to try openjdk from e...
-
SkyWarrior commented,
Using only a single sample as PON will probably won't yield any good results using GATK Somatic Copy Number variation workflow. You might want to try other tools such as Control-Freec or varscan wh...
-
SkyWarrior commented,
Hi Y R Is that only a single sample provided to the FilterIntervals tool? You need to provide all related samples at the same time to this tool not in a for loop seperately.
-
SkyWarrior commented,
Here is the issue I believe. There seems to be a discrepancy between NGS data and its annotated form in ENSEMBL, Annovar, GnomAD and elsewhere vs dbSNP. Looking at the refseq transcript on hg38 vs...
-
SkyWarrior commented,
Hi shiyi Du My initial thoughts about this was a simple left alignment of sequences during variant call and annotation however it does not seem so. Obviously sanger reference seems to have extra ba...