A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference
<p>We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional "reference genome", incorporating known variation within a species. Our goal is to support the inference o...
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| Format: | Conference item |
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Springer
2016
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| _version_ | 1797088776985509888 |
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| author | Iqbal, Z Maciuca, S del Ojo Elias, C McVean, G |
| author_facet | Iqbal, Z Maciuca, S del Ojo Elias, C McVean, G |
| author_sort | Iqbal, Z |
| collection | OXFORD |
| description | <p>We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional "reference genome", incorporating known variation within a species. Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis.</p> <br/> <p>Our scheme results in an increased alphabet size, and by using a wavelet tree encoding of the BWT we reduce the performance impact on rank operations. We give a specialised form of the backward search that allows variation-aware exact matching. We implement this, and demonstrate the cost of constructing an index of the whole human genome with 8 million genetic variants is 25GB of RAM. We also show that inferring a closer reference can close large kilobase-scale coverage gaps in P. falciparum.</p> |
| first_indexed | 2024-03-07T02:54:54Z |
| format | Conference item |
| id | oxford-uuid:aeef5bed-d1e4-4298-9dbd-961384b72edf |
| institution | University of Oxford |
| last_indexed | 2024-03-07T02:54:54Z |
| publishDate | 2016 |
| publisher | Springer |
| record_format | dspace |
| spelling | oxford-uuid:aeef5bed-d1e4-4298-9dbd-961384b72edf2022-03-27T03:46:12ZA natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inferenceConference itemhttp://purl.org/coar/resource_type/c_5794uuid:aeef5bed-d1e4-4298-9dbd-961384b72edfSymplectic Elements at OxfordSpringer2016Iqbal, ZMaciuca, Sdel Ojo Elias, CMcVean, G<p>We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional "reference genome", incorporating known variation within a species. Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis.</p> <br/> <p>Our scheme results in an increased alphabet size, and by using a wavelet tree encoding of the BWT we reduce the performance impact on rank operations. We give a specialised form of the backward search that allows variation-aware exact matching. We implement this, and demonstrate the cost of constructing an index of the whole human genome with 8 million genetic variants is 25GB of RAM. We also show that inferring a closer reference can close large kilobase-scale coverage gaps in P. falciparum.</p> |
| spellingShingle | Iqbal, Z Maciuca, S del Ojo Elias, C McVean, G A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference |
| title | A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference |
| title_full | A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference |
| title_fullStr | A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference |
| title_full_unstemmed | A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference |
| title_short | A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference |
| title_sort | natural encoding of genetic variation in a burrows wheeler transform to enable mapping and genome inference |
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