User: Len Trigg

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Len Trigg1.5k
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Posts by Len Trigg

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Answer: A: RTG vcfeval: number of variants reported by vcfeval is not equal to actual numbe
... By default, vcfeval excludes variants that are not `PASS` or `.` in the VCF `FILTER` column (you can use `--all-records` if you want to include these). There are other variant classes that are out-of-scope for the matching process, such as SVs, very long indels, non-variant records (i.e. `GT` is ` ...
written 4 months ago by Len Trigg1.5k
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Answer: A: VCF evaluation using RTG.jar vcfeval
... Just circling back here for anyone coming from the future :-) The `--sample` flag can be used to specify which sample to select from the baseline or calls VCF in the case of multi-sample VCFs. Check the vcfeval user manual for more information. ...
written 4 months ago by Len Trigg1.5k
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Comment: C: Correct reference for Platinum Genomes?
... When we (RTG) processed that data several years ago to produce our own segregation phased variant call set, I recall there were some difficulties processing the BAM files. (We were converting the BAMs back to reads so we could process through our whole mapping/variant calling pipeline, and had to pu ...
written 9 months ago by Len Trigg1.5k
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Answer: A: Can a command in RTG (or elsewhere) annotate the TP/TN/FP/FN's produced from RTG
... Yes, that's easy, just use `--output-mode annotate` (also check out the other output modes in case something else is more suitable to your needs). ...
written 9 months ago by Len Trigg1.5k
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Comment: C: VCF - what are overlapping variants?
... In VCF, column 4 is REF and 5 contains the ALT alleles - while Pierre's example doesn't contain the other columns that would be needed to make it valid VCF, I would assume that is what he is intending. In which case the first variant (CATA to C) would represent a three base deletion (the ATA are no ...
written 17 months ago by Len Trigg1.5k
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Comment: C: why is variant calling difficult?
... It's worth noting that this inherent representational ambiguity is also why _matching_ variants (for example looking up called variants in a variant database, intersecting two variant call sets to find common vs different variants, evaluating variant caller accuracy with respect to a gold standard b ...
written 21 months ago by Len Trigg1.5k
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Answer: A: Create a pseudo-haploid fasta file based genotype calls for an individual (vcf f
... Fairly close is `rtg samplereplay` from [RTG Tools][1], which generates a "pseudo-genome" for an individual based on the genotypes in the VCF, e.g.: # Make test data $ cat <ref.fa >seq ATAAATTCCC EOF # RTG likes to store sequence data in it's "SDF" format: $ rtg fo ...
written 2.0 years ago by Len Trigg1.5k
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Answer: A: Simulating Trio Data
... You could use the simulation tools available in [RTG Tools][1]. I would recommend running the `demo-tools.sh` script that comes as part of the package, as that steps through an end to end simulation of genomes of family members. You can then modify things from there according to your needs. In parti ...
written 2.3 years ago by Len Trigg1.5k
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Answer: A: Identifying De Novo Mutations from vcf files
... Here's how I would do it with [RTG Tools][1]. This assumes your samples are named "father", "mother", "son" with their calls contained in block-compressed, tabixed VCFs named father.vcf.gz, mother.vcf.gz, son.vcf.gz respectively: rtg vcfmerge father.vcf.gz mother.vcf.gz child.vcf.gz \ --a ...
written 2.3 years ago by Len Trigg1.5k
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Comment: C: Constructing a mean ROC curve based on 5 iterations
... This seems off-topic for biostars? Perhaps more appropriate to ask on [stats.stackexchange.com][1] [1]: https://stats.stackexchange.com/ ...
written 2.4 years ago by Len Trigg1.5k

Latest awards to Len Trigg

Appreciated 3 months ago, created a post with more than 5 votes. For C: VCF header line counting
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Variant call format (VCF) file, how to get statistics per sample?
Scholar 9 months ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Appreciated 15 months ago, created a post with more than 5 votes. For C: VCF header line counting
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: VCF header line counting
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Appreciated 20 months ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Appreciated 2.6 years ago, created a post with more than 5 votes. For C: VCF header line counting
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Supporter 2.7 years ago, voted at least 25 times.
Appreciated 2.8 years ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Guru 2.8 years ago, received more than 100 upvotes.
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Scholar 3.0 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Should you decompose and normalize multi-allelic variants for comparison / ID as
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: VCF header line counting
Scholar 3.2 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Appreciated 3.2 years ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: intersect VCF files
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP
Scholar 3.4 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP

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