User: d-cameron

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d-cameron570
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1 year, 6 months ago
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Posts by d-cameron

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Is there any robust way to convert VCFs to SQL (for easier comparisons) in R or
... Many of the problems with VCF comparisons will not be solved by just putting the information into a database. The difficultly of VCF comparison is, at least in part, due to the ability to represent events in multiple ways. For example, a VCF containing a 1bp deletion and SNV 10bp upstream can be equ ...
written 26 days ago by d-cameron570
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Comment: C: annotation of SV (Structural Variants)
... Somatic calling Leaderboard results are publicly available at https://www.synapse.org/#!Synapse:syn312572/wiki/61509 ...
written 28 days ago by d-cameron570
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Comment: C: annotation of SV (Structural Variants)
... The GRIDSS paper focused on germ-line results, but most of our applications have been in cancer genomics and GRIDSS did manage to win the ICGC-TCGA DREAM Somatic Mutation Calling Challenge (SV sub-challenge #5). See https://github.com/PapenfussLab/gridss/blob/master/example/somatic.sh for very basi ...
written 28 days ago by d-cameron570
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Answer: A: annotation of SV (Structural Variants)
... SVs are problematic for many pipelines/software as, unlike SNVs and small indels, each event involves at least two genomic loci. Be aware that not all callers correctly classify events. Many callers will classify events purely on their break-end position and orientation. This results in deletion ca ...
written 28 days ago by d-cameron570
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Comment: C: Base call from BAM file
... > all the possible overlapping bases with my reference dataset How do you define indel overlap? > I would like to perform a base calling and not a variant calling How does this differ from setting the flag on your favorite variant caller to also output homozygous reference calls? > This ...
written 28 days ago by d-cameron570
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Comment: C: How is the FM-index built for multiple entries of a fasta file?
... The [bwa paper][1] includes pseudo-code for some steps, although probably not the particular step you are interested in. [1]: https://academic.oup.com/bioinformatics/article/25/14/1754/225615/Fast-and-accurate-short-read-alignment-with ...
written 4 weeks ago by d-cameron570
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Answer: A: How is the FM-index built for multiple entries of a fasta file?
... 1) the bwa implementation treats the genome as a single linear sequence 2) in bwa, this is stored as text in the .amb and .ann files. Each aligner will have their own conventions 3) software implementations take some time to familiarise yourself with. In the case of bwa, short variable names, ters ...
written 4 weeks ago by d-cameron570
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Answer: A: somatic variant calling with no germline sample
... Are you looking for sensitive identification of all somatic variants, particular actionable variants (eg gene fusion breakpoints), or signs of large-scale events such as chromothripsis? If you're happy to control your FDR by accepting a low sensitivity and ignoring small to medium sized indelsthen ...
written 5 weeks ago by d-cameron570
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Answer: A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
... This depends on the relative cost of false positives vs false negatives. What FDR and sensitivity are you aiming for? I've done some fairly extensive benchmarking of SV callers for which you can find germ-line and simulation results at http://shiny.wehi.edu.au/cameron.d/sv_benchmark to given you so ...
written 5 weeks ago by d-cameron570
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Comment: C: What are the sematics of containing bwa split read alignments?
... The primary alignment is given in the SA tag: 19 mismatches (10 bases soft clipped), nominal mapq of 9. The issue is that bwa is reporting it as a split read alignment using the `SA` tag, not an alternate alignment using the `XA` tag. There's also 6 alternate alignments in the XA tag that I removed ...
written 5 weeks ago by d-cameron570

Latest awards to d-cameron

Scholar 28 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 5 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 5 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 7 weeks ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 5 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

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