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crg+bcbio sources vcfanno config from:
- [x] wgs reports (panel, panel-flank):
1. ~/crg/crg.vcfanno.{conf,lua}
2. /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/config/v…
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Looks like vcfanno is adding a '/' to the beginning of a file name (note the file is a symbolic link) that I provided in the conf file. When I point the conf to to absolute path everything works fine…
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[[postannotation]]
fields=["af_exac_all", "af_exac_afr", "af_exac_amr", "af_exac_eas", "af_exac_nfe", "af_exac_oth", "af_exac_sas"]
op="max"
name="max_aaf_all"
type="Float"
I am trying to do similar …
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Hi,
I am getting all `-1` scores in the output vcf. To check if the software is installed correctly, I have then tried running the tests in `tests/test.sh` . The last one passes (I think) but the fir…
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Variants classified as [known pathogenic variants on MitoMap ](https://www.mitomap.org/foswiki/bin/view/MITOMAP/ConfirmedMutations) are being annotated as "likely benign" in the "MitoTip_interpretatio…
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Hi,
I am trying to annotate my VCF file (biallelic SNPs only, edited to remove the chr prefix of the chromosome name for each variant to match the CADD naming convention) with CADD v1.6 and running…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.1.1
- OS name and version (`lsb_release -ds`): Ubuntu 18.04.6 LTS
**To Reproduce**
Exact bcbio command you have used:
```
mul…
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Hello 👋 , I'm getting this error when using https url.
Here is the error:
```
vcfanno.go:113: [Flatten] unable to open file: /https://raw.githubusercontent.com/nf-core/test-datasets/modules/data…
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**Describe the bug**
`vep` currently occupies whole node and uses fraction of it.
**To Reproduce**
**Expected behavior**
**If workflow, which rules**
`vep_somatic`
`vep_germline`
…
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Greetings,
I'm trying to install bcbio v1.2.8 on an AWS cluster, but upon running upgrade to install the aligners and genomes, I'm getting this error: 2021-10-28 00:44:02 ERROR 404: Not Found
```…