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(py3venv) [fi1d18@cyan01 fi1d18]$ samtools mpileup -q 1 -f /hs37d5.fa 1.bam 2.bam > 1.pileup
[mpileup] 2 samples in 2 input files
Set max per-file depth to 4000
Killed
(py3venv) [fi1d18@cyan01 f…
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Hi there,
we're trying to install bcbio with the below command:
python bcbio_nextgen_install.py /shared/pipeline-user/bcbio --tooldir=/shared/pipeline-user/tools/local --genomes hg38 --aligners bw…
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bcbioadmin@ip-10-0-0-44> bcbio_nextgen.py -v
1.1.5a
bcbioadmin@ip-10-0-0-44> tail bcbio-nextgen.log
[2019-04-15T16:57Z] multiprocessing: calculate_sv_bins
[2019-04-15T16:57Z] multiprocessing: …
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The following recipes have `meta.yaml` files that are breaking the nightly upload job. The order for sections in a `meta.yaml` should be `package`, `source`, `build`, `requirements`, `test`, `about`, …
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- WES copy number calling
- probably with varscan
- https://github.com/genome/cncwl
- This re-runs varscan on the bam. Investigate whether the varscan output files being created in detect va…
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Hello everyone!
When I try the command below,and the warning occur.
```
perl vcf2maf.pl --input-vcf 001.vcf --output-maf 001.maf --ref-fasta /Public_Resources/Illumina_Genome/iGenome/Homo_sapien…
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Tried to install using the latest stable version of bcbio-nextgen but it exists with an error. See further down below for complete error message.
System is Centos 7.6.1810
Installation of bioco…
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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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```
root@a231da4504f2:~/notebooks/neoepiscope# neoepiscope call -x ~/neoepiscope.data/hg19 -d ~/neoepiscope.data/gencode_v29/ -c adjusted_hap_som_germ.out -a HLA-A -o tests/output_prediction_somatic_…
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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 …