User: d-cameron

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d-cameron500
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Posts by d-cameron

<prev • 61 results • page 1 of 7 • next >
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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 3 days ago by d-cameron500
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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 3 days ago by d-cameron500
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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 4 days ago by d-cameron500
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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 4 days ago by d-cameron500
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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 days ago by d-cameron500
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What are the sematics of containing bwa split read alignments?
... I'm parsing the output of bwa (0.7.15) and I'm getting some split read alignments that seem very strange. For example, take the following redacted record: ReadName 2115 chrUn_JTFH01001478v1_decoy 12 1 250M chr21 10325621 0 * * NM:i:13 SA:Z:chr21,10325808,-,240M10S,9,19; The read is aligned to ...
sa split read bwa written 5 days ago by d-cameron500
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Comment: C: Deciding on a Variant Caller
... It's pretty easy to outperform 5 other callers when you get to select the data set, the truth set, and the callers to compare against. ...
written 12 days ago by d-cameron500
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Answer: A: Deciding on a Variant Caller
... Have a look the results of the DREAM Somatic Mutation Calling Challenge [1]. There are a number of somatic-only callers that perform well on their benchmarks. [1] http://dreamchallenges.org/project/icgc-tcga-dream-somatic-mutation-calling-challenge/ ...
written 12 days ago by d-cameron500
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Answer: A: memory consumption of bwa-mem
... Close to 8GB is a fairly typical index size for a human reference gnome [1]. If poor performance is acceptable, or the memory usage is only just over 8GB, you may wish to considering increasing and/or adding additional swap space to allow bwa to run. Be aware that amplicon sequencing has artefacts ...
written 17 days ago by d-cameron500
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Answer: A: NGS overlapping reads
... Your question is somewhat unclear as to what sort of read overlap you are referring: - Reads from different read pairs overlapping the same reference sequence. These reads originate from different fragments of different copies of the same DNA template. For human, your input library will contain ma ...
written 17 days ago by d-cameron500

Latest awards to d-cameron

Scholar 4 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 4 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 19 days ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 4 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

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