giraffe-sv-paper

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SV calling using giraffe/vg

1

It's not very clear to me how exactly VG or Giraffe carries out SV calling (if it truly does). The tutorials mention how we can do genotyping using existing SV...

tnnandi

readSVvcf is not work in findDups.R

4

Hello, I want to construct the SV graph from several assemblies. Before starting my own works, I am testing the pipeline according to your manual, [first merge SVs from multiple...

zhqduan

Hello, When I repeat the example you provided, I updated my Sveval version to 1.2.1 and a new problem occurred. This error message is‘Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key...

xiaoguizz

1000 Genomes related SV calls

2

Hi, Many thanks for making all code and data available. I am very keen to access this file (https://cgl.gi.ucsc.edu/data/giraffe/products/vggiraffe-sv-relkgp-raw.vcf.gz) reflecting the SV calls from the related subjects in 1000 Genomes....

samkleeman1

QUESTIONS in code of SV genotyping

2

Hi, When I was converting the cram to the fastq, I found the code in your WDL workflow: > seq 0 ~{in_nb_chunks} | head -n ~{in_max_chunks} | parallel -j ~{in_cram_convert_cores}...

NMUzhoujun

Error running vg construct on GIAB_0.6 sample ->> error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph

1

Hi, I am trying to run and replicate the giraffe SV paper results for GIAB 0.6 sample, to genotype SVs from the Illumina paired reads. I am currently following the...

rbr7