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https://gnomad.broadinstitute.org/gene/ENSG00000012048?dataset=gnomad_r2_1_non_cancer
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Hi
We are trying to make new echtvar file.
The following are the command and error:
./echtvar encode gnomad.exomes.r2.1.1.sites.only.controls.norm.vcf.gz gnomad.json gnomad.exome.r2.1.1.sites.o…
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When trying to annotate with Haplogrep2, it complains because INFO contains whitespace from gnomAD. Source gnomAD VCF already contains this, so I need to fix it at the Dockerfile.
Exception is as …
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Thank you for SnpSift, what a powerful useful program! I'm new to SnpSift, and have a basic question - the VCF file I'm starting with already has an INFO.AF field. I want to annotate the VCF file with…
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Hi,
I noticed that a `allele` json field is reported for matched variants in custom annotation with the `exact` method. However it is not reported when the `overlap` method is used instead. Please se…
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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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Hello,
I have been using Exomiser for some time but have a specific issue that is causing some confusion:
I have a list of a handful of variants (1-3) that I want to input into Exomiser and esse…
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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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I'm using this script:
```
#!/bin/bash
# Parameters to replace:
# The GOOGLE_CLOUD_PROJECT is the project that contains your BigQuery dataset.
GOOGLE_CLOUD_PROJECT=psjh-eacri-data
INPUT_PATTER…
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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…