Journal: Nature Communications

Article Title: A diploid assembly-based benchmark for variants in the major histocompatibility complex

doi: 10.1038/s41467-020-18564-9

Figure Lengend Snippet: a We regenotyped DeepVariant (DV) heterozygous SNVs with WhatsHap using Oxford Nanopore Technologies (ONT) and PacBio HiFi (CCS) reads to find a confident set of SNVs with concordant genotypes from DV/CCS, WhatsHap/ONT, and WhatsHap/CCS—our Confident HETs for phasing. We selected 10x Genomics (10X) variants with phased blocks from the 10X VCF. For phasing, we used WhatsHap to combine phased blocks from 10X with ONT reads to get a single phased block across the MHC. b We binned PacBio HiFi reads into two haplotypes, which are denoted as orange and blue reads, using WhatsHap. c We performed diploid assembly using the Peregrine Assembler with the haplotype-binned HiFi reads. d We generated the benchmark variant callset from the assembled haplotigs using dipcall, and defined benchmark regions excluding SVs, exceptionally divergent regions, low-quality regions in the assembly, and long homopolymers.

Article Snippet: This v4.1 benchmark uses a similar variant integration approach to the previous version , but v4.1 adds mapping-based variant calls from the 10x Genomics and PacBio HiFi datasets used in this work to expand to regions difficult to map with short reads.

Techniques: Blocking Assay, Generated, Variant Assay

Journal: Nature Communications

Article Title: A diploid assembly-based benchmark for variants in the major histocompatibility complex

doi: 10.1038/s41467-020-18564-9

Figure Lengend Snippet: a Proportion of 10 randomly selected FPs and 10 randomly selected FNs from 11 callsets from Illumina (Ill), 10x Genomics (10x), PacBio HiFi (PB), and Oxford Nanopore (ONT) that were determined to be fully correct in the benchmark and incorrect or only partially correct in the query callset. b Breakdown of variants potentially incorrect in the benchmark or correct in the query, where curation of the benchmark determined it to be incorrect (no), correct (yes), or unclear (unsure).

Article Snippet: This v4.1 benchmark uses a similar variant integration approach to the previous version , but v4.1 adds mapping-based variant calls from the 10x Genomics and PacBio HiFi datasets used in this work to expand to regions difficult to map with short reads.

Techniques:

Journal: Nature Communications

Article Title: A diploid assembly-based benchmark for variants in the major histocompatibility complex

doi: 10.1038/s41467-020-18564-9

Figure Lengend Snippet: The CCS-DeepVariant VCF from PacBio HiFi reads incorrectly filters the 2-bp deletion and 9 of the 13 SNVs in the region (filtered variants are light gray boxes). The benchmark correctly calls this complex variant, and represents it as a 26-bp insertion of a TG tandem repeat followed by a 29-bp deletion of adjacent tandem repeats. When comparing this VCF to our MHC benchmark, the benchmark insertion and deletion variants are counted as false negatives, while the 5 SNVs called are counter-intuitively counted as false positives because the other variants are incorrectly filtered. If the CCS-DeepVariant VCF had not filtered all of the other variants, all variants would be counted as true positives.

Article Snippet: This v4.1 benchmark uses a similar variant integration approach to the previous version , but v4.1 adds mapping-based variant calls from the 10x Genomics and PacBio HiFi datasets used in this work to expand to regions difficult to map with short reads.

Techniques: Variant Assay

Journal: Nature Communications

Article Title: A diploid assembly-based benchmark for variants in the major histocompatibility complex

doi: 10.1038/s41467-020-18564-9

Figure Lengend Snippet: PacBio HiFi reads used in evaluation of benchmark.

Article Snippet: This v4.1 benchmark uses a similar variant integration approach to the previous version , but v4.1 adds mapping-based variant calls from the 10x Genomics and PacBio HiFi datasets used in this work to expand to regions difficult to map with short reads.

Techniques: