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Here is a strange case of a missing gnomAD variant, 17-41228120-T-C. It appears in the gnomAD browser (https://gnomad.broadinstitute.org/variant/17-41228120-T-C?dataset=gnomad_r2_1_non_cancer), but n…
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Hey there,
I'm noticing when using make-gnotate with multiple gnomad vcf.gz files which you described as such:
```
slivar make-gnotate --prefix gnomad-2.1 \
--field controls_nhomalt:gnoma…
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Hello, Brent!
Thanks for the very useful vcfanno tool!
I'd like to start using it for annotation of structural variants (SV) in the same way how it works for small variant vcf files.
Recently…
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Sub-ticket for gnomAD v4 update https://github.com/ClinGen/gene-and-variant-curation-tools/issues/47
The gnomAD link out in the VCI is now pointing to the genomic coordinates of the variant in gnom…
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Some senior members are taking these credible set chr:pos listings in PheWeb and looking up the rsIDs in Gnomad, so seems would be a better use of of their time if they were just listed in the table.
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G'day. Thanks for making a nice tool.
I'm trying to use `vcfanno` (0.3.5, linux binary) with a large combined VCF of gnomad v3.1. The combined bgzipped file is ~2TB, so obviously manipulating it is…
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subprocess.CalledProcessError: Command '['/BCBIO/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/media/data/SeaDB/BCBIO', '--genomes', 'hg38', '--aligners', 'bwa', '--datatarget', 'gemini', '--…
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Hello, I'm doing this :
vcf_input2 = pysam.VariantFile("vcf_B.vcf.gz",'r')
rec = next(vcf_input2.fetch())
print(rec.info["AC"])
print(rec.info["AF"])
when I print AG I get the same data that…
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http://gnomad-api.broadinstitute.org/
Note that we don't have a strategy for graphql yet...