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Hi,
I am trying to view SEG file in IGV. I modified the cbs file generated by varScan to match the example.seg in the IGV manual [SEG file format](https://software.broadinstitute.org/software/igv/S…
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As far as germline CNV, we will definitely need something other than Varscan. xhmm is what Ira's group has used. We should look into that and ask around for other recommendations. Haley Abel would be …
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ABSOLUTE uses the following file sets:
```
tables/%.strelka_varscan_indels.tab.txt
tables/%.$(call SOMATIC_VCF_SUFFIXES,mutect).tab.txt
```
whereas the MUTATION_SUMMARY uses a curated collection of …
hxrts updated
5 years ago
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Hello,
I tried to run nasp but after i gave all asked informations nasp just print "total_mem = 62"
It seems something is not working at the beginning of the pipeline and it ends in several secon…
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These cover variants with an 3x indel where the addition/deletion is in the middle of the codon (instead of between two codons like `inframe_insertion` and `inframe_deletion`). Thus, this type of inde…
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- [x] FASTQC v0.11.5
- [x] Trimmomatic 0.36
- [x] BWA 0.7.15
- [x] bwa mem
- [ ] bam-readcount 0.8.0
- [x] samtools 1.7
- [ ] GATK 3.8-1-0-gf15c1c3ef
- RealignerTargetCreator
…
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The current `CallSet.call_method` is incorrectly filled in for MC3 data. It should be on method per callset, but right now its a concatenation of all the methods that made common calls, leading to a w…
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I use bcftools to generate mplileup file as samtools are deprecated recently. It worked after remove the firtstline of pileup file. But the pilefile is super huge 100G plus, it's quit time-consuming …
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Hi,
When attempting to create a fresh bcbio install, I see the following:
```
Reading packages from /export/home/ncit/external/a.mizeranschi/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/contrib…
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Hello!
A fresh install of bcbio-nextgen 1.1.5 with --nodata and without --tools went well
(I removed the environments from old installations in ~/.conda/environments.txt, cleaned PATH and PYTHONP…