User: rbagnall

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rbagnall1.7k
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Posts by rbagnall

<prev • 128 results • page 1 of 13 • next >
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Comment: C: Merging genomic databases from different intervals (GenomicsDBImport)
... 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 rbagnall1.7k
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Comment: C: Is there a database of haploinsufficiency scores or status for each gene?
... yes, [here][1] [1]: https://dosage.clinicalgenome.org/help.shtml#review ...
written 4 months ago by rbagnall1.7k
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Answer: A: Is there a database of haploinsufficiency scores or status for each gene?
... [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 rbagnall1.7k
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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 rbagnall1.7k
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Comment: C: Discrepancy between UCSC table browser PhyloP score and Bedmap mapped PhyloP sco
... 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 rbagnall1.7k
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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 ...
written 8 months ago by rbagnall1.7k • updated 8 months ago by _r_am32k
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Answer: A: Figure out genotype from VCF line
... 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 rbagnall1.7k
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Comment: C: combining / merging overlapping reads in bam file to one in silico long read
... 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 rbagnall1.7k
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Answer: A: combining / merging overlapping reads in bam file to one in silico long read
... 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 rbagnall1.7k
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Answer: A: determine exon number from variant genomic coordinates
... [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 rbagnall1.7k

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Scholar 4 months ago, created an answer that has been accepted. For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Grep A Pattern From File
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Scholar 8 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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