User: Len Trigg

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Len Trigg1.5k
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Posts by Len Trigg

<prev • 100 results • page 2 of 10 • next >
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Comment: C: compare SV results across samples - Manta, Delly
... That's a nice demo app! ...
written 2.7 years ago by Len Trigg1.5k
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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 2.7 years ago by Len Trigg1.5k
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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 2.7 years ago by Len Trigg1.5k
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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 2.8 years ago by Len Trigg1.5k
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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 2.9 years ago by Len Trigg1.5k
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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 2.9 years ago by Len Trigg1.5k
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Comment: C: VCF Normalisation is required ?
... Both hap.py and vcfeval perform comparison at the level of underlying haplotypes asserted by the entries in the VCF, so they don't require up-front normalization. Normalization is mostly useful if you are trying to do comparisons using tools that don't operate at the haplotype level (but such tools ...
written 3.0 years ago by Len Trigg1.5k
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Answer: C: SMaSH installation error
... Isn't SMaSH basically abandoned? You may be better to use the benchmarking tools developed by GA4GH which are now widely used, see https://github.com/ga4gh/benchmarking-tools ...
written 3.0 years ago by Len Trigg1.5k
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Comment: C: Strategies to call variants from a cancer sample
... You might like to try the `rtg somatic` command from [RTG Core][1]. It uses a Bayesian model to jointly call the normal and tumor, including options to output both germline variants as well as gain-of-reference (potential somatic reversion) calls. As well as the primary score fields produced by the ...
written 3.1 years ago by Len Trigg1.5k
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Comment: C: Edditing headers from a .vcf.gz file
... Decompressing and recompressing with gzip is slow as it is typically limited to one core (although see `pigz` and `pbgzip`). If the VCF were block compressed it would technically be possible to decompress just the block(s) containing the VCF header, write it out with the edited header, and then dire ...
written 3.1 years ago by Len Trigg1.5k

Latest awards to Len Trigg

Appreciated 5 months ago, created a post with more than 5 votes. For C: VCF header line counting
Good Answer 7 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 11 months ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
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 17 months ago, created a post with more than 5 votes. For C: VCF header line counting
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: VCF header line counting
Teacher 19 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 22 months ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 2.4 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 2.7 years ago, created a post with more than 5 votes. For C: VCF header line counting
Good Answer 2.8 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 2.9 years ago, voted at least 25 times.
Appreciated 2.9 years ago, created a post with more than 5 votes. For C: VCF header line counting
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
Guru 3.0 years ago, received more than 100 upvotes.
Teacher 3.1 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 3.2 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Good Answer 3.2 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 3.2 years ago, created a comment with at least 3 up-votes. For C: VCF header line counting
Scholar 3.3 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Appreciated 3.3 years ago, created a post with more than 5 votes. For C: VCF header line counting
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: intersect VCF files
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP
Scholar 3.6 years ago, created an answer that has been accepted. For A: GATK's Join Genotyping workflow on a large pedigree
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Variant calling for MNP

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