User: Len Trigg

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Len Trigg1.3k
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Posts by Len Trigg

<prev • 96 results • page 1 of 10 • next >
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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 4 months ago by Len Trigg1.3k
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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 8 months ago by Len Trigg1.3k
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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 12 months ago by Len Trigg1.3k
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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 15 months ago by Len Trigg1.3k
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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 16 months ago by Len Trigg1.3k
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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 16 months ago by Len Trigg1.3k
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Comment: C: compare SV results across samples - Manta, Delly
... That's a nice demo app! ...
written 18 months ago by Len Trigg1.3k
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Comment: C: compare SV results across samples - Manta, Delly
... The SVanalyzer `SVcomp` tool does take repeat homology into account since it constructs the resulting haplotypes and compares them. I haven't tried it myself yet, so am not sure whether it also works with non-sequence-resolved calls though. ...
written 18 months ago by Len Trigg1.3k
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Answer: A: compare SV results across samples - Manta, Delly
... Comparing SVs across callers is certainly not an easy problem. There is active work in the GIAB consortium around deriving high quality SV call sets and developing tools for comparing call sets, so there are several options under current development. You will probably end up trying a few tools to se ...
written 18 months ago by Len Trigg1.3k
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Comment: C: MAF vs VAF
... Yes, and I would favour the term Variant Allele Fraction (or Variant Allelic Fraction) rather than Variant Allele Frequency for this reason too! ...
written 20 months ago by Len Trigg1.3k

Latest awards to Len Trigg

Teacher 7 weeks 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 3 months ago, created a post with more than 5 votes. For C: VCF header line counting
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: VCF header line counting
Teacher 4 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 8 months ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 15 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 19 months ago, created a post with more than 5 votes. For C: VCF header line counting
Good Answer 20 months 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 20 months ago, voted at least 25 times.
Appreciated 21 months ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 21 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
Guru 21 months ago, received more than 100 upvotes.
Teacher 23 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
Scholar 2.0 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Good Answer 2.1 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 2.1 years ago, created a comment with at least 3 up-votes. For C: VCF header line counting
Scholar 2.2 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Appreciated 2.2 years ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: intersect VCF files
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP
Scholar 2.4 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP
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 3.0 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
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP

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