GIAB calls cancelled during government shutdown

[justi...@gmail.com]

Dear GIAB Analysis Team,

Due to the ongoing government shutdown, the GIAB call on Monday is cancelled. 

Want to help keep the work of the Genome in a Bottle Consortium moving while our NIST team is on furlough? We have several draft germline and somatic benchmarks that you can help evaluate and give critical feedback to improve!

1. Somatic v0.4 draft benchmarks for clonal structural and copy number variants in the new GIAB pancreatic tumor cell line HG008. By using paired tumor/normal assemblies, we have precisely resolved and phased complex SVs, as well as SVs in VNTRs. For more information about how to use these, see readme and files at https://lnkd.in/eEYaJuWY

2. Somatic v0.2 draft benchmark for clonal small variants in HG008. Again, the assemblies helped us resolve somatic variation in homopolymers, tandem repeats, and segmental duplications that most variant callers miss even though they are clonal. Many of the repeat-associated indels are hard to represent and compare in VCF, so let us know if you have ideas for this!
VCF at https://lnkd.in/eN5jh4bv.
Benchmark BED at https://lnkd.in/ejTNdN7H.
More conservative BED that excludes somatic variants that modify germline variants (e.g., if a 1bp germline INS changes to a 2bp INS in the tumor) at https://lnkd.in/e_f7qWni.

3. Germline benchmarks for small variants and/or SVs for GRCh37, GRCh38, and T2T-CHM13 derived from the highly polished T2T HG002 assembly, which we plan to release after the shutdown as our v5.0 GIAB benchmarks (see collaborative preprint with the T2T consortium about the assembly and a new genome benchmarking technique as well https://lnkd.in/eYK-zRsj!) A version of the benchmark similar to what we plan to release as v5.0 is at https://lnkd.in/ep5P52gM (see README for comparison guidance)

Hoping we will be back at work soon to incorporate your suggestions and finalize these benchmarks, and thanks for your support!

Justin