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Recent Replies
Answer: using GRanges metadata to constrain overlap searches between objects
by
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Rather than do all overlaps all the time for all samples, why not restrict the data by sample when you can. The code below works about 4 ti…
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Tom
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Hello, thank you for your answer,
I have a question, Why the information from the GFF file and from the feature table is different? I see …
Comment: 1000 genomes hg38 with dbSNP rsid
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It should be pretty straightforward. Just to save you some pain, run these on the 1000g VCF once you download it:
1. `vt decompose -s` to …
Comment: 1000 genomes hg38 with dbSNP rsid
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Yeah, I had some hope that I wouldn't need to mess with doing this ...
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> Hi all,
>
> I have a sam file, my supervisor asked me to count the number of
> unmapped reads, which command I should use?
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> sam…
Comment: 1000 genomes hg38 with dbSNP rsid
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In that case, you'll need to get the VCF from 1000g - that's probably going to be the only place where individual level data is available, …
Comment: 1000 genomes hg38 with dbSNP rsid
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Actually, I need the VCF file with the individual level data, not the sites file.
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No, not yet. But next to each ACMG entry there is an explanation why it is (or not) called.
I'll contact with authors to ask them to at l…
Comment: 1000 genomes hg38 with dbSNP rsid
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Thanks! For posterity, it may be unclear to others what genome version this is. It is indeed hg38 as `wget -O- -q https://ftp.ensembl.org/p…
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The error message is quite difficult to parse,
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Hi @shreyiitgn
The way the module-trait relationship works with categorical variables is well explained in this [blog][1].
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The one on the Ensembl ftp site have rsids.
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❯ wget -O- -q https://ftp.ensembl.org/pub/current_variation/vcf/homo_sapiens/1000GENOME…
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