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When running the CombineVariants command the `set` INFO field retains information about each caller that contained the variant. When we run CombineVariants a second time, the only information is that …
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### Subject of the issue
the depth not right, much less than the
### Your environment
samtools 1.3.1 or 1.5
### Steps to reproduce
/gpfs/software/pipeline/pipeline/tools/samtools mpileup…
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## Bug Report
Here is an issue that one of our users found: https://github.com/ga4gh/dockstore/issues/569
Basically, the cwl is invalid as `inputBinding` does not belong under `arguments`; however, …
k-cao updated
7 years ago
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I tried to install bcbio_nextgen on 2 different macs and on a cluster. In each case, I always get the same error (described below), where the package age-metasv seems to be absent. However, I have alr…
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Hi,
I'm getting an error in the variant calling pipeline, can you please help with this? Here is the traceback:
```
[2017-03-06T21:55Z] Configuring 1 jobs to run, using 1 cores each with 3.50g …
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Hi Brad,
Could you take a look at this issue pls? I was trying to download mm10 genome - the download contains a file called homo_sapiens_merged_vep_90_GRCh37.tar.gz so I don't understand why the e…
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Hi, what is the default minimal support reads for bcftools to call a snp/indel? I found that there is an indel in my sample with two support reads, it seems that bcftools will not consider it as an in…
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Hi
I am having errors on multiple Perl scripts on OS X with Perl 5.18.2
```
This is perl 5, version 18, subversion 2 (v5.18.2) built for darwin-thread-multi-2level
(with 2 registered patches, see p…
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We either need to:
1. Natively support CRAM throughout the workflow
2. Convert back to BAM first thing
3. Convert back to BAM only for steps that require BAM instead of CRAM
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Hi Brad,
My bcbio run has been unable to proceed past a certain T-N paired sample at the prioritisation step, up to the generation of the manta tsv files. I checked the commands and can't find anyt…