User: Len Trigg

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Len Trigg1.2k
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Posts by Len Trigg

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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 3 months ago by Len Trigg1.2k
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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 6 months ago by Len Trigg1.2k
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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 6 months ago by Len Trigg1.2k
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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 7 months ago by Len Trigg1.2k
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Comment: C: compare SV results across samples - Manta, Delly
... That's a nice demo app! ...
written 9 months ago by Len Trigg1.2k
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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 9 months ago by Len Trigg1.2k
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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 9 months ago by Len Trigg1.2k
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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 11 months ago by Len Trigg1.2k
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Comment: C: Can you assume variants not in VCF are all monomorphic for the reference allele?
... It's worth noting that assuming hom-ref if coverage exceeds some threshold is a reasonable heuristic in most cases, the real situations can be more subtle. For example, the alignments at a site may have predominantly low MAPQ, or alternatively the alignments may contain enough mismatches that a conf ...
written 11 months ago by Len Trigg1.2k
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Answer: A: Indel concordance from different VCF files
... Normalization such as left-aligning indels can help for simple cases, but these are not the state of the art for VCF comparison. This is a clear case where you should be using a haplotype-aware VCF comparison tool. As well as being able to deal with situations where an indel is placed at a different ...
written 12 months ago by Len Trigg1.2k

Latest awards to Len Trigg

Teacher 6 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 10 months ago, created a post with more than 5 votes. For C: VCF header line counting
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Appreciated 12 months ago, created a post with more than 5 votes. For C: VCF header line counting
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Scholar 15 months ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
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Scholar 2.6 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
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