marbl / hg002 Goto Github PK

Hi,
I'm currently working on benchmarking VCF files generated from HG002_data(test_run just one sample) for SV calling(Manta, lumpy, GRIDSS, nf-core/sarek) against a truth set. I aligned the BAM files using GRCh38. Any ideas on how to effectively benchmark my results on which truth set?
Thank you.

Is Nanopore raw data available for this?

I was looking for it!

https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.0.1.fasta.gz

Hi @skoren,

As always amazing work!

as per the read me file -- "The assembly used [verkko](https://github.com/marbl/verkko) with manual assignment of nodes to chromosomes, ONT-based patching to resolve HiFi coverage gaps, manual resolution of tangles, and Strand-Seq and Hi-C based assignment of acrocentric short arms to chromosomes."

If I want to follow similar approach for an assembly, where I can find the details of these steps? ex: how the nodes were assigned to chromosome or how tangles in the graphs were resolved?

Thank you

It would be nice if the HG002 reference files were ordered in a more aesthetically pleasing fashion. Currently we have:

$ zcat hg002v1.0.fasta.gz | grep ">"
>chr10_MATERNAL
>chr10_PATERNAL
>chr11_MATERNAL
>chr11_PATERNAL
>chr12_MATERNAL
>chr12_PATERNAL
>chr13_MATERNAL
>chr13_PATERNAL
>chr14_MATERNAL
>chr14_PATERNAL
>chr15_MATERNAL
>chr15_PATERNAL
>chr16_MATERNAL
>chr16_PATERNAL
>chr17_MATERNAL
>chr17_PATERNAL
>chr18_MATERNAL
>chr18_PATERNAL
>chr19_MATERNAL
>chr19_PATERNAL
>chr1_MATERNAL
>chr1_PATERNAL
>chr20_MATERNAL
>chr20_PATERNAL
>chr21_MATERNAL
>chr21_PATERNAL
>chr22_MATERNAL
>chr22_PATERNAL
>chr2_MATERNAL
>chr2_PATERNAL
>chr3_MATERNAL
>chr3_PATERNAL
>chr4_MATERNAL
>chr4_PATERNAL
>chr5_MATERNAL
>chr5_PATERNAL
>chr6_MATERNAL
>chr6_PATERNAL
>chr7_MATERNAL
>chr7_PATERNAL
>chr8_MATERNAL
>chr8_PATERNAL
>chr9_MATERNAL
>chr9_PATERNAL
>chrEBV
>chrM
>chrX_MATERNAL
>chrY_PATERNAL

Hi,
If I want to generate a phased Nanopore BAM file, should I directly map the Nanopore reads against HG002, so the reads will be mapped to paternal or maternal chromosomes, or should I map against CHM13, then phase the reads base on heterozygous SNP as usual ?