User: rbagnall
rbagnall • 1.7k
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Posts by rbagnall
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... I don't think you can merge GenomicDBs.
Instead, you should create the interval-based GenomicsDBImport databases, then genotype each one to give multiple vcfs, then merge the vcfs. ...
written 23 days ago by
rbagnall • 1.7k
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... yes, [here][1]
[1]: https://dosage.clinicalgenome.org/help.shtml#review ...
written 4 months ago by
rbagnall • 1.7k
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... [ClinGen Genome Dosage Map][1] is manually curating genes and regions of the genome to review the evidence for haploinsufficiency and triplosensitivity, and then score each accordingly. They have completed ~1500 genes and genome regions so far, so perhaps one to watch.
The probability that a gene i ...
written 4 months ago by
rbagnall • 1.7k
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Answer:
A: VQSR no r file being created
... Is the `all_jointcalls_sorted_AS.tranches` file made?
have you put the `\` afterwards, to separate from the `--rscript-file` command?
If the `all_jointcalls.AS.plots.R` file is created, try to run it afterwards, with
`Rscript /path/to/all_jointcalls.AS.plots.R`
...
written 4 months ago by
rbagnall • 1.7k
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... Which human genome build is the data from? The second method used `hg19` - is this the same genome build as the first method?
Which conservation scores did you use? The first method uses
> 100 Vert. Cons" description="100 vertebrates Basewise Conservation by
> PhyloP"
The second method uses ...
written 7 months ago by
rbagnall • 1.7k
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Comment:
C: Figure out genotype from VCF line
... The last column shows the genotype
1/1:0,29:29:87:1131,87,0
the `1/1` means the genotype is `T/T`
a `0/0` would be `C/C`
a `0/1` would be `C/T`
the `0,29` means there were 0 reads with a C and 29 with a T
Have a look at the [VCF specifications][1] to understand the other columns
[1]: ht ...
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... Two things to help you:
> But what exactly does "T,<\non_ref>" mean in the ALT column?
You have only made a `g.vcf` file with `HaplotypeCaller`. This is a file that is 'poised' to be genotyped, but that has not yet been performed. You need to use the `g.vcf` file as input in the genotypi ...
written 8 months ago by
rbagnall • 1.7k
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... Can you get the reference genome to which your BAM file is aligned? I'm not sure how you could join together the sequence using only the example format from above. ...
written 8 months ago by
rbagnall • 1.7k
0
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1
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309
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... After `bedtools merge`, you could pipe the output into [bedtools getfasta][1]
[1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 8 months ago by
rbagnall • 1.7k
1
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1
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302
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1
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... [VEP][1]. You will need the GRCh37 build for the shown variant
Put the genomic position in the 'input data' box, reformatted like so `16 20359634 20359634 C/G`
Make sure you select the 'exon and intron numbers' option. The variant will be in different exons, depending on the transcript.
[1]: h ...
written 8 months ago by
rbagnall • 1.7k
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For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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12 months ago,
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For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Popular Question
13 months ago,
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For LOD score of a single genotype
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14 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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15 months ago,
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For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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For C: How to extract specific chromosome from vcf file
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created an answer that was upvoted at least 5 times.
For A: Grep A Pattern From File
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For LOD score of a single genotype
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3.5 years ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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4.5 years ago,
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For C: How to extract specific chromosome from vcf file
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For A: Trouble filtering CDS regions from Nextera Enrichment design
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