-
When I run varscan somatic using a reference genome with a large number of contigs (>2000) the program completes without error, but does not output data in the outfile files for all the contigs. All …
-
@t-neumann @jkobject While running `slamdunk all` of the [jkobject/slamdunk](https://github.com/jkobject/slamdunk/tree/master) fork on a set of 10 samples, slamdunk doesn't produce tcount files for 2 …
-
Exception in thread "main" java.lang.NumberFormatException: For input string: "156051AAA>E;BBEEDDEEEEBEEEDEECEDE'@CD?CEEEEEE@DEDEEEEDEDEEEEE>C@FDE:EC6CEEEEFDEEECD/EBDEEEDDEEEEECADEDDDADDB"
at java…
-
There are pipeline scripts for these tools, but when i run i get a message saying that these are not available
ERROR:: The pipeline (CNV-freec) you have placed in the SEG file is not currently supp…
-
Hi,
I am trying to run varscan 2.4.2 in somatic mode:
```
java -jar /opt/varscan/VarScan.v2.4.2.jar somatic \
normal.pileup tumor.pileup \
/opt/varscan/output/normal-tumor. \
--min-coverage 3 -…
-
There are currently two separate wrappers for [SAMTOOLS MPILEUP](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/samtools/mpileup.html) and [VARSCAN MPILEUP2SNP](https://snakemake-wrapper…
-
When I ran QC3 on my exome vcf files generated through mpileup/VarScan, the consistency tables is showing very high (>0.9) for all sample pairs, meaning all samples are contaminated with each other as…
-
As in varscan's default txt output, there are more stats info including filtering for high confident variants, that would be helpful for mucor to support this input format like it supports mutect's tx…
-
We have observed that shards of varcan work are sporadically failing and not being caught by Cromwell.
This manifests as statements like this in the Varscan stderr:
```
[E::bgzf_read_block] Fail…
-
Thanks Dan for the great tool,
I just noticed what I think are typos in the accompanying doc
bash variables with $ in front and spaces at either sides of the '=' sign
Best
Stephane
```
htt…