RT Journal Article
SR Electronic
T1 A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 059170
DO 10.1101/059170
A1 Sorina Maciuca
A1 Carlos del Ojo Elias
A1 Gil McVean
A1 Zamin Iqbal
YR 2016
UL http://biorxiv.org/content/early/2016/07/25/059170.abstract
AB We show how positional markers can be used to encode genetic variation within aBurrows-Wheeler Transform (BWT), and use this to construct a generalisation ofthe traditional “reference genome”, incorporating known variation within aspecies. Our goal is to support the inference of the closest mosaic of previouslyknown sequences to the genome(s) under analysis.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.