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The current seqr sample qc pipeline does not apply hard filters in the `get_qc_mt` function: https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/sampl…
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Hi, I'm wondering if one can use gnomad instead of 1k-genomes for the ancestry estimate. somalier files for thousand genomes are restricted to only 5 superpopulations whereas gnomad has a higher diver…
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Katie brought to our attention that in EFL1:
This long deletion variant exists in genomes only, and can be found by searching for it:
https://gnomad.broadinstitute.org/variant/15-82225077-TCCGTGCC…
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As part of adding a Provisional Evidence subtile, we want to add a description to the [Allele Frequency Reference Sets Tile help section](https://brcaexchange.org/help#allele-frequency-reference-sets)…
e-t-k updated
2 months ago
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Currently, gnomAD can only be browsed by Ensembl genes / transcripts. It should also support RefSeq genes / transcripts.
This only applies to gnomAD v3.1+. This requires VEP annotations with RefSeq…
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Hello,
thank you for providing this great tool.
i'm running the tool with the following command but got an error:
```
$ svafotate annotate -v my_file.fit.vcf -o my_file.fit.pop.vcf -b /home/d…
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1. It looks like the dictionary contains entries for the gnomAD hemizyous counts (e.g. Allele_count_hemi_exome_AMR_GnomAD) but the build file doesn't contain these counts.
2. There appears to be a mi…
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Hi @brentp
I am having the same issue reported on [issue#94](https://github.com/brentp/slivar/issues/94).
I downloaded gnomad v3.1.1, and concat all the chr VCF into one file, around 2.3T.
…
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Some collaborators are testing our service and some queries aren't working as expected with this endpoint. We should see what kinds of variants aren't supported + try to resolve these issues.
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Since there is no gnomAD vvp build anymore I tried to run the example build (which works in the example provided), it gives segmentation error in my own vcf file which I formatted as it is in the exam…