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Hi Christoffer,
Here is an unexpected question for you :P
As I understand it, superFreq uses the reference normal samples for two purposes:
a) To calculate the differential coverage over captu…
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Hi,
I was trying to upgrade [bcbio-nextgen](https://bcbio-nextgen.readthedocs.io/en/latest/) package using the following command:
```
python bcbio_nextgen_install.py /home/jshi/local/share/bcbio …
jxshi updated
5 years ago
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Hi. I am trying to run the pipeline, but keep getting this error despite adding Picard to the path (CLASSPATH) as suggested. Please help.
I have fulfilled all dependencies, and surprisingly Varsca…
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Hello,
I'm getting several errors (below) when running joint VC with Strelka2 in bcbio-nextgen v.1.1.3 (stable). HaplotypeCaller works fine on my input data.
It also looks like Platypus isn't be…
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I was able to successfully run bcbio_nextgen on one of my sample data. For the most part everything looks great, except I do not seem to have any calls or vcf files from scalplel and pindel. I set ind…
bwubb updated
6 years ago
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All the old scripts - vphaser, diversi, varscan, freebayes to VCF scripts should be put in here.
along with the vcf stats/filters etc
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I try to identify false positive varscan2 (v2.4.3) somatic calls
I adapted the command listed in the Koboldt et al, Curr Protoc Bioinfo 2013 p8 (PMID 25553206) and it does not output.
```
bam-…
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Now that there are cliffs marked in bed files under `bam/*.bed`, varscan should read read these files to know an additional kind of place to mask SNP calls.
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Hello. I'm sorry if it is a trivial question.
When I performed paired analysis, there were so many variants comparing other analysis softwear because most of the variants were 0 or very low read in n…
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Dear @everestial,
First, first things... I love this script! Thanks a lot! Then, go to the problem: I've converted an initial VCF to table (and all worked perfectly) but in the inverse process (ta…