User: Chris Saunders

gravatar for Chris Saunders
Reputation:
180
Status:
Trusted
Location:
Illumina
Website:
https://www.linkedin.c...
Twitter:
@ctsa11
Last seen:
11 months ago
Joined:
6 years, 4 months ago
Email:
c********@illumina.com

Rare disease and cancer analysis models for NGS data, Illumina staff scientist:

https://www.linkedin.com/in/christophertsaunders

Posts by Chris Saunders

<prev • 13 results • page 1 of 2 • next >
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Answer: A: strelka2 vs strelka1
... Some general points: - The Strelka2 passing somatic variant thresholds are set to be more sensitive than the default pass settings for Strelka1, so a specificity drop would not necessarily be surprising depending on the sample, however it would be concerning if you found results were still subopti ...
written 19 months ago by Chris Saunders180
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Answer: A: Strelka output: read count of REF and ALT, SNVs
... A note on this topic has been added to Strelka2 user guide here: https://github.com/Illumina/strelka/tree/master/docs/userGuide#somatic-variant-allele-frequencies ..this should still be applicable to the older Strelka release. ...
written 2.5 years ago by Chris Saunders180
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Answer: A: Questions about the splitting/spannings reads reported by manta
... Regarding RNA-specific concerns, please note that Manta's RNA-Seq capability is currently under development and is not supported. Given that context, I hope some additional detail will be helpful: First note that the genotype is "0/0" here, so this isn't a variant call. minEdgeObservations is the ...
written 2.9 years ago by Chris Saunders180
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Answer: A: Difference between the two models in manta
... The short answer is that the germline model assumes a diploid sample with corresponding allele frequencies. The tumor-only model assumes the variant could occur at any allele frequency. The best starting point for a high-level overview is the user guide: https://github.com/Illumina/manta/tree/maste ...
written 2.9 years ago by Chris Saunders180
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Comment: C: Merging consecutive non-variant calls
... Sorry, don't know of anything that would do this right out of the box.. ...
written 3.5 years ago by Chris Saunders180
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Answer: A: Merging consecutive non-variant calls
... It has not been maintained for current GATK, but this tool is designed to merge any non-variants from GATK 1.x all-sites output: https://sites.google.com/site/gvcftools/home/configuration-and-analysis/gatk_to_gvcf-usage ...
written 3.5 years ago by Chris Saunders180
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Answer: A: detecting putative t-dna insertion from genome sequencing data from Arabidopsis
... You might try detecting insertions with manta: https://github.com/Illumina/manta (full disclosure: I'm an author). This is a general purpose SV and indel caller which includes insertion detection -- it will report both fully assembled insertions and "imprecise" insertion points where a putative inse ...
written 3.5 years ago by Chris Saunders180
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Comment: C: Tools for SV & CNV detection
... Re: Manta, note default configuration is WGS -- enrichment/panel analysis requires `--exome` config option: https://github.com/Illumina/manta/blob/v0.29.3/src/markdown/mantaUserGuide.md#exometargeted ...
written 4.0 years ago by Chris Saunders180
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Answer: A: How To Get Count Of 0|0 From A Gvcf
... Using the latest gvcftools, you can run: gzip -dc genome.vcf | ${GVCFTOOLS_BIN}/extract_variants --invert | ${GVCFTOOLS_BIN}/get_called_regions >| homref_regions.bed ...
written 6.0 years ago by Chris Saunders180
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Answer: A: Query Gvcf Against My Variants
... Hi, You can get the gvcftools package here: https://sites.google.com/site/gvcftools/home/download This package contains the 'break_blocks' tool which will extract a set of sites overlapping with the regions in bed file -- this seems like it could cover your workflow. As an example, if you format ...
written 6.2 years ago by Chris Saunders180

Latest awards to Chris Saunders

Good Answer 2.0 years ago, created an answer that was upvoted at least 5 times. For A: Converting Gvcf Files Into Vcf
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Converting Gvcf Files Into Vcf
Autobiographer 4.4 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Converting Gvcf Files Into Vcf

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