User: d-cameron

gravatar for d-cameron
d-cameron880
Reputation:
880
Status:
Trusted
Location:
Australia
Last seen:
2 weeks, 4 days ago
Joined:
2 years, 1 month ago
Email:
d***************@gmail.com

Posts by d-cameron

<prev • 102 results • page 1 of 11 • next >
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Comment: C: Help in writing NGS pipeline (or: the road from fasta to vcf)
... That pipeline will detect SNVs and small indels. You may also be interested in detecting copy number changes, larger structural variants, or other variants in regions (such as microsatellites and telomeres) requiring specialised variant callers. ...
written 18 days ago by d-cameron880
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Comment: C: finding variants in the low to no coverage areas of bacterial genomes
... It's still possible that you have other types of SVs (e.g. inversions, duplications, translocations). Also, pindel can't detect insertions larger than ~100bp (it depends on the read length) so if you have a large insertion (e.g. of a new gene) you'll still miss it. A caller designed to detect comple ...
written 18 days ago by d-cameron880
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Comment: C: IGV does not show BAM file information
... Delete any .bai index file, convert to SAM, then to CRAM. It might also be worth trying samtools (v1.6) to generate the CRAM if you're having issues. ...
written 22 days ago by d-cameron880
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Answer: A: What does <*> mean in a vcf file?
... >In short, ALT (alternative allele) is set to be "<>". From the VCF specification, * indicates a deletion, while brackets indicate some sort of ID string. To me, none of these make much sense, and here the depth is 1 - how can there be any variants here? (For actual polymorphic sites, ALT i ...
written 23 days ago by d-cameron880
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Comment: C: finding variants in the low to no coverage areas of bacterial genomes
... Have you considered indels or larger structural variants? You may have your variant hiding in plain sight if you're not looking for indels or SVs. ...
written 23 days ago by d-cameron880
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Answer: A: IGV does not show BAM file information
... Indexed BAM access is limited to chromosomes shorter than 512Mb. You need to chop your reference chromosomes up such as they are all smaller than 512Mb, or convert your BAMs to CRAM (or SAM but then they'd be huge). ...
written 23 days ago by d-cameron880
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Answer: A: Is there any read-mapping package that could map only the first half or the seco
... bwa mem performs split read alignment and, for the reads where the breakpoint is indeed in the middle, will report two alignments for the one read. I've found that bwa doesn't report them all. I found that feeding the non-split-read soft clipped alignments back into bwa gives additional split read a ...
written 5 weeks ago by d-cameron880
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Answer: A: MAPQ filtering for clinical applications
... >Remember that this is a clinical setting where a result can change a person's life. As the analyst, would you sign your name on a clinical report, a document type that has legal weight, in knowing that you let these low MAPQ reads through? Would you sign your name on a clinical report that said ...
written 9 weeks ago by d-cameron880
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Answer: A: VIew reads sorted by name in IGV
... >I can visually compare the alignments IGV displays all alignments _relative to the reference genome_. The x axis in IGV is always reference genome coordinates. IGV will never display a read that is not aligned to the reference genome. > I have two sets of alignments from different sequencin ...
written 9 weeks ago by d-cameron880
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Comment: C: NGS data simulation: VarSim or BAMSurgeon?
... Just ART from FASTA files. I created script to generate the FASTA files since VarSim only supports simple ins/del/dup/inv SVs. Entire classes of somatic mutations (gene fusion, chromoplexy/chromothripsis/breakage-fusion-bridge, double minutes, ...) were missing from the simulators the last time I c ...
written 9 weeks ago by d-cameron880

Latest awards to d-cameron

Centurion 18 days ago, created 100 posts.
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 9 weeks 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.
Scholar 5 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.
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: annotation of SV (Structural Variants)
Scholar 6 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.
Scholar 8 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 8 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 8 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 8 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.
Scholar 12 months ago, created an answer that has been accepted. For A: bwa and bowtie2 bamfile format
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Please, please, define what a 'read' is.

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