User: d-cameron
d-cameron • 2.0k
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Posts by d-cameron
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... > How do I parse the raw data of VCF in R?
You already know the answer to that: it's the `readVcf()` function. You use the `VariantAnnotation` library to fully parse the file, or you use a text file parser if you need the raw input lines for some reason (you very rarely do).
See [here][1] for ...
written 5 days ago by
d-cameron • 2.0k
0
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... What is the larger problem that you are attempting to solve, and why only hard clips, not soft clips?
Wouldn't it be easier to just use a utility such as `gridss.ComputeSamTags SOFTEN_HARD_CLIPS=true` to convert your hard clips into soft clips then do you conversion to BED? ...
written 10 weeks ago by
d-cameron • 2.0k
0
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... IF you really want to use bowtie2, The GRIDSS SV caller includes a gridss.SoftClipsToSplitReads utility program that will feed the soft clipped portion of the reads back to an aligner of your choice and convert them to split reads. Even works on the output of bwa which, somewhat surprisingly, result ...
written 10 weeks ago by
d-cameron • 2.0k
2
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1
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200
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... Note that a CNV can be caused by more complex events that just simple duplication or deletions. For somatic SV in cancer, SVs are frequently caused my complex catastrophic rearrangements such as chromothripsis and chromoplexy. In such cases, paired flanking primers around the breakpoint are likely t ...
written 10 weeks ago by
d-cameron • 2.0k
0
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2
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2.0k
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2
answers
Comment:
C: What does <*> mean in a vcf file?
... Unfortunately, the specs do not explicitly state whether the symbolic allele includes explicitly listed alt alleles or not. ...
written 10 weeks ago by
d-cameron • 2.0k
0
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2
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1.7k
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2
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... The DELLY authors updated their output to use BND notation (which is good) but they only write one of the two records required for a valid VCF BND breakpoint (which is bad).
Technically my tool is doing the correct thing but that isn't particularly useful for users. I have a few other projects taki ...
written 11 weeks ago by
d-cameron • 2.0k
0
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2
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1.6k
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2
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... Unfortunately not. We do have a benchmarking paper with more comprehensive results coming out soon. ...
written 11 weeks ago by
d-cameron • 2.0k
0
votes
1
answer
254
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1
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... > gns <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
genes(hg19) returns some really strange results. You'll want to use transcripts() instead as some genes are annotated have two transcripts 100+Mb apart so genes() matches almost the whole chromosome for those.
The clinical pipelines I'm invol ...
written 7 months ago by
d-cameron • 2.0k
2
votes
5
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602
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5
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... This question is actually very well timed. The GAG4H file formats working group has an upcoming teleconference on the future of VCF and a potential new file format. I strongly recommend getting involved if there are limitations in the existing file formats that make it unsuitable for your use case. ...
written 7 months ago by
d-cameron • 2.0k
1
vote
0
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316
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0
answers
... You have redirected the bwa standard error output stream (stderr) to the same location as the standard output stream (stdout. Check your bwa command as redirects such as `2>&1` will do this.
Check your shell configuration as well as some configurations will perform this redirect automaticall ...
written 8 months ago by
d-cameron • 2.0k
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For A: Please, please, define what a 'read' is.
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For A: Modernising the FASTQ Format
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For GRIDSS: the Genomic Rearrangement IDentification Software Suite
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For A: Please, please, define what a 'read' is.
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For A: annotation of SV (Structural Variants)
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