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Hi Brad;
I would like to know if I can use this standalone software on VCF called algorithms other than (vardict, freebayes, mutect, varscan) ? My VCF belong to the same version 4.0.
My aim is to f…
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Hi Brad,
**I met the follow bus error, which stopped the bcbio running.**
2017-01-26T00:45Z] c2819.***.edu: Timing: hla typing
[2017-01-26T00:47Z] c2819.***.edu: Timing: alignment post-processin…
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Hi, I ran freebayes, scalpel, varscan and vardict for ensemble calling, but I ended up getting the error below. Is there any solution without rerunning the whole calling procedure from the beginning. …
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I believe that I'm getting the same error as https://github.com/chapmanb/bcbio-nextgen/issues/1154 ,see traceback below.
```
2016-01-22T12:02Z] Varscan
[2016-01-22T12:02Z] [mpileup] 1 samples in 1 in…
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Hi, I'm getting errors from a run with both tumor-only and tumor-normal samples:
[2015-12-11T09:56Z] Use of uninitialized value $sample in concatenation (.) or string at /usr/local/share/bcbio/anacon…
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Thank you so much for pushing the fix for the segfault! When trying to update using bcbio-nextgen.py upgrade --tools, I got this fatal error:
Traceback (most recent call last):
File "/share/PI/eua…
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unable to install on m4.4XL instance
"sudo python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37 --aligners bwa" aborts see below:
Please consider posting the…
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Hi,
I'm trying to run bcbio for germline variation. I ran it before without a hitch, but for some reason I now get an error I can't decipher:
> [2016-11-10T16:50Z] Identified 156 parallel analys…
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As MuTect 1 is not compatible with Java 8 (throws a lot of errors) I'd like to point the pipeline to a Java 7 version (the one installed systemwide). Setting
``` yaml
resources:
java:
bin…
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Dear There,
I tried to use bcbio_nextgen.py to detect mutation by four callers (mutect, varscan, freebayes, vardict) for exon sequencing data. But I ran into the below error.
##### ERROR ------------…