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After discussion in #3084, I offer myself to port the indel realignment pipeline. After exploring the GATK3 implementation, I will split the port in the following independent tasks:
- [ ] Port `Rea…
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Gold standard benchmarking datasets such as the GIAB/NIST NA12878 and the Illumina Platinum Genomes truth sets provide both a VCF containing the variant records themselves, plus a BED file of "high co…
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When running the pipeline, I get methylation classification results in the GUI, but there are several errors in the terminal. CNV data is missing, and I cannot generate a report from the GUI. I have a…
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Hi, I am trying to use octopus for liquid biopsy samples. In this context I have deep (10,000x) targeted (~1.3Mb Panel) sequencing data which are preprocessed by deduplication and bqsr (gatk). So cove…
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Hey Ian,
This is just a thought. I realize that the smith-waterman to both haplotypes helps sort out alignment edge effects with indels, but does it do anything for SNPs? I realize that a nearby in…
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@tprodanov, I want to reconstruct the haplotypes from MHC region. I have used the following commands.
````bash
jellyfish count --canonical --lower-count 2 --out-counter-len 2 --mer-len 25 --threads …
gsc74 updated
2 months ago
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Hi,
I am using minimap2 to map long ONT reads (up to 400Kbp), and I am finding that the supplementary chaining is producing large rearrangements in the read sequence, flipping strands, and jumping …
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Apologies if this is covered somewhere and I missed it, but I couldn't find information about using a phased HiFi + Hi-C Hifiasm assembly as input for GreenHill. Would it be considered haplotype-aware…
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Hello,
I'm using MUMandCO to call SVs between the homologous chromosomes of my haplotype-phased genome assembly. I'm particularly interested in duplications and inversions. I ran the program using …
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Hello vg team
I am trying to run a haplotype-expression analysis using rpvg.
I am using a spliced-pangenome and a pantranscriptome that have already been created. The respective pangenomes and fil…