User: d-cameron
d-cameron • 850
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Posts by d-cameron
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... >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 4 days ago by
d-cameron • 850
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... >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 4 days ago by
d-cameron • 850
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... 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 4 days ago by
d-cameron • 850
0
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1
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... Hard clipping removes the read base and quality information from that record in the BAM file. It must be recovered from another source (e.g. the original FASTQ file) as the information is not present in the BAM file.
Exception: if the BAM file contains multiple record for a single read, the hard cl ...
written 9 days ago by
d-cameron • 850
1
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3
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351
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Answer:
A: Structural Variant annotation
... The 'standard' format for reporting SVs is the [VCF file format][1] using the `SOMATIC` flag (note that not all callers will actually write that flag). Converting VCF SVs into MAF is problematic since the MAF format appears to only support single-loci indel SV events. I recommending not converting t ...
written 11 days ago by
d-cameron • 850
1
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3
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Comment:
C: Structural Variant annotation
... The only 'standard' we have is the [VCF file format specifications][1]. Unfortunately, the standardized fields do not include the fields required for a breakdown of the SV support by type (split read, discordant read pair, one-end anchored read, assembled breakend contig, assembled breakpoint contig ...
written 11 days ago by
d-cameron • 850
1
vote
3
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351
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3
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Comment:
C: Structural Variant annotation
... > I understand what a VCF/BCF format is, but my annotation has columns named split read support and tumor split read support and tumor variant allele count
These are not standard VCF SV fields and are specific to DELLY. The standard VCF fields can be found in the [VCF file format specifications] ...
written 11 days ago by
d-cameron • 850
0
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2
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275
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... You want flags in which the 5 least significant bit is either set or unset.
https://broadinstitute.github.io/picard/explain-flags.html
In awk, you'd probably want to do something like `and(16, $FLAGS) != 0` ...
written 28 days ago by
d-cameron • 850
1
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2
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275
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... Reads can align to either strand so you'll actually need two filters: one where the soft clip is at the end of the CIGAR and the read aligned to negative strand flag is not set, and another when the soft clip is at the start of the CIGAR and the negative strand flag is set. ...
written 29 days ago by
d-cameron • 850
0
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1
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176
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1
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... The default settings should be fine. Are you using doing pair-end sequencing, or just single end? If you just have single end reads, then GRIDSS is unlikely to do any better than a purely split read based caller (e.g. CREST). Due the issues with ctDNA I have outlined above, you may find that it migh ...
written 29 days ago by
d-cameron • 850
Latest awards to d-cameron
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
3 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: annotation of SV (Structural Variants)
Scholar
4 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
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.
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: filtering structural variants from normal-tumor pairs (whole-genome sequencing)
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
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.
Teacher
6 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
6 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
Scholar
10 months ago,
created an answer that has been accepted.
For A: bwa and bowtie2 bamfile format
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Please, please, define what a 'read' is.
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