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. 2014 Oct;30(19):2813-5.
doi: 10.1093/bioinformatics/btu376. Epub 2014 Jun 6.

ABRA: improved coding indel detection via assembly-based realignment

Lisle E Mose  1 , Matthew D Wilkerson  2 , D Neil Hayes  2 , Charles M Perou  2 , Joel S Parker  2
Affiliations

ABRA: improved coding indel detection via assembly-based realignment

Lisle E Mose et al. Bioinformatics. 2014 Oct.

Abstract

Motivation: Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative.

Results: We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation.

Availability and implementation: ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra.

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Figures

Fig. 1.
Fig. 1.
Mendelian consistent loci and Mendelian conflict rates for Freebayes and UnifiedGenotyper both pre- and post-ABRA. UnifiedGenotyper results with GATK Local Realignment around Indels as well as HaplotypeCaller results are also shown for comparison. Shapes in this figure represent variant depth, whereas color/shading represent caller and realignment method
Fig. 2.
Fig. 2.
Concordance/discordance with TIGRA assembled contigs for predicted calls from FreeBayes (pre- and post-ABRA), Pindel and Haplotype Caller. Indels within the ranges enabled by ABRA are evaluated (deletions up to 2000 bp and insertions up to the read length). The numbers in the figure represent a cutoff point for variant quality scores as reported in the respective caller’s VCF output. A small number of pre-ABRA deletions >30 bp and 0 pre-ABRA insertions >30 bp are called. FreeBayes currently does not use reads partially overlapping an insert as supporting evidence, which may impact post-ABRA sensitivity for longer insertions
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