{"id":701,"date":"2023-11-02T16:17:51","date_gmt":"2023-11-02T16:17:51","guid":{"rendered":"https:\/\/terrabioappdev.wpenginepowered.com\/boosting-variant-calling-in-terra-with-the-new-telomere-to-telomere-human-reference\/"},"modified":"2023-12-27T04:56:02","modified_gmt":"2023-12-27T04:56:02","slug":"boosting-variant-calling-in-terra-with-the-new-telomere-to-telomere-human-reference","status":"publish","type":"post","link":"https:\/\/terra.bio\/boosting-variant-calling-in-terra-with-the-new-telomere-to-telomere-human-reference\/","title":{"rendered":"Boosting Variant Calling in Terra with the New Telomere-to-Telomere Human Reference"},"content":{"rendered":"

There is a new, more complete human reference on the <\/span>Terra reference disk<\/span><\/a>!<\/span><\/p>\n

When the Human Genome Project was declared complete in 2003, there were a number of gaps in the reference, due to the repetitive nature of much of the human genome and limitations of technologies available then. This left approximately 8% of the human genome out of the canonical reference sequence. To fill this gap, the <\/span>first complete sequence of a human genome<\/span><\/a> \u2013 also known as the Telomere-To-Telomere (T2T) reference \u2013 was announced, in early 2022. The T2T reference was built using a multitude of latest sequencing technologies to expose the missing 8%. It lets scientists access even the trickiest regions like centromeres, segmental duplications, and other complex regions, including around 100 new protein-coding genes. In addition to these <\/span>gains, some errors found in the previous GRCh38 reference are corrected resulting in an overall higher quality reference. Simply switching to this reference improves variant calling performance (see this <\/span>writeup<\/span><\/a>).\u00a0<\/span><\/p>\n

Scientific Background<\/b><\/p>\n

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Building a reference sequence is a special type of assembly project, involving multiple modes of orthogonal technologies to generate data and careful analysis. In the case of the T2T reference, the CHM13 (complete hydatidiform mole) haploid human cell line was used to assemble the autosomes and the X chromosome. The <\/span>full Y chromosome<\/span><\/a> sequence was included in 2023 using DNA from a sample commonly known as HG002 (also frequently referred to as NA24385). A few versions of the T2T reference were included in the <\/span>data release<\/span><\/a> to facilitate different types of analyses. These differ in a handful of ways described below.<\/span><\/p>\n

The maskedY<\/b> Reference<\/b><\/p>\n

The pseudo-autosomal regions (PAR) are a pair of regions on chrX and chrY. Because they are homologous to each other, alignments to these regions are ambiguous, and end up with much lower mapping quality for both. Traditionally, one would mask the corresponding regions on chrY for all samples, and produce diploid variant calls in the PAR on chrX. The maskedY version of the T2T reference does just this, and replaces the PAR on chrY with hard-masked N bases so users can readily align their reads coming from these regions.<\/span><\/p>\n

The rCRS Sequence<\/b><\/p>\n

The T2T release includes a new mitochondrial sequence derived from the CHM13 cell line. An alternate version, containing the old revised Cambridge Reference Sequence (<\/span>rCRS<\/span><\/a>) chrM sequence identical to the one in the human reference hg38, is included in this version of the T2T release. This is convenient for backwards compatibility with mitochondrial studies done with hg38.<\/span><\/p>\n

The EBV Sequence<\/b><\/p>\n

The Epstein-Barr virus (EBV) sequence is included as chrEBV in our version of the reference provided on Terra. This is consistent with our curated hg19 and hg38 reference files, as described in <\/span>our reference documentation<\/span><\/a> and following conventions from the All of Us project. This contig is useful during alignment for siphoning off viral sequence common in human samples and helps improve data quality for samples from lymphoblastoid cell lines like the Corielle 1000 Genomes samples.<\/span><\/p>\n

How to use the T2T Reference on Terra<\/b><\/p>\n

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You\u2019ll find our recommended version of the T2T reference for most use cases on Terra under the name \u201cT2T-v2.\u201d The v2 corresponds to the T2T release v2.0, which includes the chrY sequence.\u00a0<\/span><\/p>\n

Our version corresponds to the following choices<\/span><\/p>\n