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It would be good to have the complete VCF files available for all the sample sets which would be beneficial. This allows that truth set does not rely on couple of interest sites, but allows for comple…
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**Describe the bug**
Unable to download mm39
**To Reproduce**
1. SnpEff version: SnpEff version SnpEff 5.2c (build 2024-04-09 12:24)
2. Genome version: mm39
3. SnpEff full command line: `java -…
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Hi!
Long time fan of your work here!
I have about 16 mitochondrial genome that I needed to find variants with, so I have been trying to use ekidna for it :)
However, I have been stuck in the …
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Hi,
I've generated VCF files from single-end FASTQ using PHEnix pipeline. Then I tried to add them to database and I got this message:
```
Namespace(command='vcf_to_db', config_file='/home/use…
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VCF downloaded here http://www.completegenomics.com/public-data/69-Genomes/ causes a parse error when running vcf2wt.
The error can be isolated to a single line vcf as follows:
```
##fileformat=VCFv…
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```
I have successfully used SKPSMTPMessage to attach files and communicate
with Gmail SMTP servers. I am, however, experiencing a strange side
affect. When I download the file from the email, on a …
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Thanks you for this great library.
But I have met some troubles. Could you help me solving it.
I have two vcf file. I want to merge those two into one file.
```
v1 = pysam.VariantFile(vc…
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### Current Behavior
This is a pretty fun bug but a bit hard to explain. Thankfully very easy to fix.
When using VCF inputs to `augur ancestral` we need a VCF file and a reference FASTA file. Th…
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Hello,
Has anyone had any issues creating contacts or calendar events lately? I am getting a bad put request and all of my contacts are being stored locally on disk instead of the collections-root. …
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Currently any non-ACGT IUPAC codes are written as an 'N'. It would be possible to keep the information by writing out multiple output genotypes for a sample, with equal probabilities.
Not yet sure …