User: d-cameron

gravatar for d-cameron
d-cameron850
Reputation:
850
Status:
Trusted
Location:
Australia
Last seen:
1 day, 7 hours ago
Joined:
1 year, 11 months ago
Email:
d***************@gmail.com

Posts by d-cameron

<prev • 95 results • page 1 of 10 • next >
2
votes
1
answer
137
views
1
answers
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 4 days ago by d-cameron850
0
votes
2
answers
117
views
2
answers
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 4 days ago by d-cameron850
0
votes
2
answers
410
views
2
answers
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 4 days ago by d-cameron850
0
votes
1
answer
110
views
1
answers
Answer: A: How to retrieve hard clipped reads
... 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-cameron850
1
vote
3
answers
351
views
3
answers
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-cameron850
1
vote
3
answers
351
views
3
answers
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-cameron850
1
vote
3
answers
351
views
3
answers
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-cameron850
0
votes
2
answers
275
views
2
answers
Comment: C: How to extract only 5-prime hard/soft clipped reads?
... 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-cameron850
1
vote
2
answers
275
views
2
answers
Comment: C: How to extract only 5-prime hard/soft clipped reads?
... 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-cameron850
0
votes
1
answer
176
views
1
answers
Comment: C: Any good SV calling software for CtDNA?
... 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-cameron850

Latest awards to d-cameron

Scholar 4 days 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.
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.
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.
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.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1458 users visited in the last hour