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-searching for reference exome (CDS) as a reference for our exome sequence data due to several reasons:
1- when we aligned to one chromosome like chr 20, the alignment rate was v.v low 2.8%
2- whe…
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A user wrote in asking about the allele numbers (AN) for this [variant](https://gnomad.broadinstitute.org/variant/3-10052405-G-A?dataset=gnomad_r4). I realized from their question that the non-UKB A…
ch-kr updated
4 months ago
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Open an exome and the stats look odd. You need to select the default bed to get something more reasonable. Can we auto detect WGS/WES and auto select bed or suggest that the user selects the bed.
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https://iobio.s3.amazonaws.com/samples/bam/NA12878.exome.bam
This is likely due to the binning. Maybe not a problem, but we need to understand what's happening
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### What you did:
I looked at the GnomAD 4.1 data for variant chr2:79195912-G-T
https://gnomad.broadinstitute.org/variant/2-79195912-G-T?dataset=gnomad_r4
### What happened:
The foot of the …
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Issue by @Anuragksingh, moved from SciLifeLab#763
> Hello,
> I had some doubts over ascat.
> It would be really helpful if you can provide some insights about that.
> Can we use the available…
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The latest Gnomad version is now 4.0.0
We are running version 2.1 for exomes and genomes, and 3.1 for mitochondria.
[Link to Gnomad download page](https://gnomad.broadinstitute.org/)
Consider wheth…
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### Description of the bug
I think the problem might be the format (using .list or .bed formats) that I used to use in intervals parameter and I do not know the correct format (even after reading the…
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@damiansm @julesjacobsen @pnrobinson @drseb
Can you please suggest or make some easy improvements?
Longer term we would like to redirect and/or mirror the Sanger online site but will leave that up …
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There aren't enough variants in the 1000g.phase3.100k set for VerifyBamID to work properly for quite a few of the exome samples I've been running. I've generated my own panel using common variants in …