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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…
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Hello, there are VCF header lines from FpFilter.java file from VarScan.v2.4.4.source.jar - looks like this is fpfilter source.
```
String vcfHeaderInfo = "";
vcfHeaderInfo = "##FILTER=";
vcfHeader…
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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…
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# Describe the bug
We have observed that ```ivar variants``` can generate false positive variant calls for SARS-CoV-2 genomes that contain insertions or deletions. Here is an example from a private…
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I see for CRISPREessoWGS you need to specify an interval in which the analysis is run on. I'm wondering if CRISPresso can be run on the entire genome (entire WGS data)?
Thanks!
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How does Varscan (v2.4.3) determine that two consecutive SNVs are part of the same event and call the variants as a MNV?
I have multiple examples where BAM files (which have gone through differing …
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I'm getting errors when trying to run Coovar. I'm not sure whether you should feed in a `.fa` file or `fa.gz` file?
I've tried both but get the following errors:
## Unzipped
```
(snakemake) …
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Running trios pipeline
```
#Create a three-sample mpileup
samtools mpileup -B -q 1 \
-f ref.fasta \
dad.bam mom.bam child.bam >trio.mpileup
#Run VarScan trio
varscan trio trio.mpileup trio.mp…
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Hi,
I ran the following code but output was in VarScan format.
TuncBook-Pro:blackhole morova$ java -jar ~/varscan/VarScan.v2.4.1.jar somatic normal/normal.mpileup tumor/tumor.mpileup --output-vcf 1…
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Hi,
I just found a wired issue with varscan and it happened to both 2.4.4 and 2.4.3. Basically the varscan vcf files have wrong DP related values, about 50% off the values reported by IGV or Mutect…