User: rbagnall
rbagnall • 1.7k
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Posts by rbagnall
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1
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1
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... yes, [here][1]
[1]: https://dosage.clinicalgenome.org/help.shtml#review ...
written 14 days ago by
rbagnall • 1.7k
2
votes
1
answer
75
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1
answers
... [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 15 days ago by
rbagnall • 1.7k
3
votes
1
answer
114
views
1
answers
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 21 days ago by
rbagnall • 1.7k
0
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0
answers
219
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0
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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 3 months ago by
rbagnall • 1.7k
0
votes
1
answer
280
views
1
answers
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 ...
3
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1
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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 4 months ago by
rbagnall • 1.7k
0
votes
1
answer
167
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1
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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 4 months ago by
rbagnall • 1.7k
0
votes
1
answer
167
views
1
answers
... After `bedtools merge`, you could pipe the output into [bedtools getfasta][1]
[1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 4 months ago by
rbagnall • 1.7k
1
vote
1
answer
190
views
1
answers
... [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 5 months ago by
rbagnall • 1.7k
2
votes
1
answer
225
views
1
answers
Answer:
A: Does Splice AI use GRCh38?
... https://github.com/Illumina/SpliceAI
The answer lies within... ...
written 5 months ago by
rbagnall • 1.7k
Latest awards to rbagnall
Scholar
21 days ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
4 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
4 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
8 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Popular Question
9 months ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
10 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
11 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Commentator
11 months ago,
created a comment with at least 3 up-votes.
For C: How to extract specific chromosome from vcf file
Centurion
2.1 years ago,
created 100 posts.
Good Answer
2.4 years ago,
created an answer that was upvoted at least 5 times.
For A: Grep A Pattern From File
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
3.2 years ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Commentator
4.2 years ago,
created a comment with at least 3 up-votes.
For C: How to extract specific chromosome from vcf file
Guru
4.4 years ago,
received more than 100 upvotes.
Scholar
4.6 years ago,
created an answer that has been accepted.
For A: Trouble filtering CDS regions from Nextera Enrichment design
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