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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.1.5
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py {CONFIG_YAML} -t ipython -n 41 -s sge -q main.r…
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using sample sheet as input. can span across multiple project folders.
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Any plans on adding VCF, gVCF, GFF, BAM, SAM or others?
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Hi, I'm trying `strelka` (version 2.9.10), and I'm running into an issue I'm having trouble debugging. The error is:
```
$ cat strelka/workspace/pyflow.data/logs/tmp/taskWrapperLogs/000/041/pyflow…
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### Description of feature
In order to deal with continuously growing number of gvcf files from haplotypecaller, it would be helpful to start the pipeline from the --joint_germline step. This would e…
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`ValidateVariants` requires a large amount of memory (>16Gb) to validate a GVCF when another GVCF is used as the interval list. This is not the case if a regular interval list is used instead. This co…
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This needs to be tested, but it appears that `merge --gvcf ref.fa` is 4x slower than `merge --gvcf -`. This may be caused by inefficient use of `faidx_fetch_seq`; would pre-loading and caching the re…
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### Description of feature
It might be useful to add a CLI-option for outputting gvcf-files instead of vcf-files. It seems that with the current version that is only possible when running `--joint_ge…
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### bug reports
hi guys :
Hi all, when I run gatk (version: 4.5.0.0) CombineGVCFs to combine 240 8 ploidy samples gvcf, it reports the error as below
![image](https://github.com/broadinst…
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GenomicsDBImport currently doesn't support multi-sample input vcfs. We've had a number of usesr request the ability to import precombined multi-sample vcfs.
People may have old call-sets which t…