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Need to decide which fields are going to be necessary in each VCF file, so that any VCF-producing script in the future can conform to standards.
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Hi,
I am using bcbio-nextgen stable version 0.9.3 for somatic variant calling, for some reason this version is unable to perform `bcbio-variation-recall ensemble` successfully.
`subprocess.CalledPro…
a113n updated
8 years ago
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From @ernfrid
fpfilter.pl appears to only be passing germline sites, which suggests to me that it was run using the NORMAL BAM.
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From @ernfrid
It looks like SOMATIC calls weren't isolated from the original VarScan run. We'll probably want to do that before running through fpfilter.pl in order to reduce unnecessary compute req…
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```
Got a divided by zero warning --
/oncoseq/lib/vs2vcf.py:102: RuntimeWarning: divide by zero encountered in log10
fields['QUAL']= str(np.around(-10 * np.log10(float(fields['QUAL'])),decimals=2))…
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Trying to install boost 1.55.0 & 1.58.0 on CentOS 7/ClusterWare 2016.01
```
[root@login1(mycluster) etc]# module avail
--- /opt/gridware/bio/el7/etc/modules ---
apps/bamtools/2.3.0/gcc-4.8.5
ap…
vlj91 updated
8 years ago
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Originally reported as BD2KGenomics/toil-scripts#58
I tried it with my varscan code, which worked fine before, and get the same `invalid pointer` issue.
My setup:
`cgcloud create-cluster --leader-in…
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after pip installing cgcloud-core, cgcloud-toil, cgcloud-mesos and s3am (all with `--pre` because otherwise I got errors), I tried
`cgcloud --help`
and got
```
ERROR: Cannot find plugin module 'cgc…
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With 0.9.6a version upon running (Illumina Trusight One Panel on MiSeq 300b.p. reads) I get the following error:
> ValueError: No callable regions found from BAM file. Alignment regions might not ove…
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Hi,
I have two bam files(normal-tumor). I would like to call variants across these samples. Since I dont require alignment I preferred bam clean and bam sort as it is suggested in the bcbio documenta…