User: d-cameron

gravatar for d-cameron
d-cameron700
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Posts by d-cameron

<prev • 78 results • page 1 of 8 • next >
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Answer: A: Are these false somatic variants? Visual inspection with IGV
... >The mutations are supported by the same reads. It's a bit suspicious to me because this could indicate that the reads are from another part of the genome. It could also indicate that there are three adjacent mutations, or another sort of mutation. Without additional context, is it difficult to ...
written 3 days ago by d-cameron700
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Comment: C: What tools do you suggest for resolving large insertions?
... >inflated estimates of translocations I've found that the majority of false positive translocations are due to sequence homology between the called location. Looking at the extent of the sequence homology around the putative translocation can give you a good indication as to whether the variant ...
written 4 days ago by d-cameron700
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Are there NGS-based CNV callers that utilise allele frequency?
... I've been attempting to find a CNV caller for WGS data that utilises both BAF and read depth but there seems to be a dearth of them. I've only managed to find PennCNV-Seq (appear to lack a corresponding publication), Weaver (cancer only, wasted a day failing to get it to run due to severe lack of do ...
cnv written 4 days ago by d-cameron700 • updated 3 days ago by Samuel Brady10
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Comment: C: What tools do you suggest for resolving large insertions?
... If you're expecting an insertion-style format, outputting as BEDPE doesn't help as you'd either have to report a pair of translocations (that VCF can already do losslessly) or result to a custom file format. If you're looking to detect novel sequence insertions then you'd need to use dedicated tool ...
written 4 days ago by d-cameron700
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Comment: C: What tools do you suggest for resolving large insertions?
... If you want to assume that all events that look like large insertions are indeed large insertions, then you should look for pairs of translocations in which a pair of translocations events occur at the same location on chrA with different orientations (technically, they with have a 1bp difference if ...
written 4 days ago by d-cameron700
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Answer: A: What tools do you suggest for resolving large insertions?
... Large insertion of sequence already in the reference, or large insertions of novel sequence (e.g. viral integration)? >Usually they falsely count them as translocations as well: for exapmle, chr2 to chr1 insertion would be reported as two translocations. I think you need to revise your expectat ...
written 4 days ago by d-cameron700
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Answer: A: Detection of CNVs from vcf file
... You should only consider this if you cannot get access to the bam files. The only tool I know of that performs what you're requesting is VCF2CNA http://biorxiv.org/content/early/2017/04/26/131235. I have not used it personally so I cannot vouch that is actually works as advertised. ...
written 5 days ago by d-cameron700
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Comment: C: How to Define Structural Variation Breakpoint Positions?
... > I was referring to a deletion on the positive strand for simplicity. Terminology can be problematic for SVs. A deletion is not 'on the positive strand' - both strands are retained or deleted. > I though CIGAR strings were for the alignment not the entire read (primary+supplementary) I use ...
written 13 days ago by d-cameron700
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Answer: A: How to Define Structural Variation Breakpoint Positions?
... The SV position you report depends on the format you report in. I strongly recommend VCF as other formats such as BED and BEDPE are ambiguous for exactly the reason you raise. The encoding of variants into VCF records is covered in the Variant Call Format (VCF) specifications document at https://sam ...
written 15 days ago by d-cameron700
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Comment: C: Filetring in vcf files
... Your genotyping filter assumes diploid. This condition is frequently violated in tumours. When you also consider tumour purity and sub-clonality, variant allele frequencies of 0.33/0.66 are perfectly normal even for diploid tumours. ...
written 15 days ago by d-cameron700

Latest awards to d-cameron

Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 15 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 8 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 9 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 9 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 11 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 6 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

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