Abstract
BackgroundCurrent variant discovery methods often start with the mapping of short reads to a reference genome; yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence. This is particularly problematic for the human leukocyte antigen (HLA) region on chromosome 6p21.3. This region is associated with over 100 diseases, but variant calling is hindered by the extreme divergence across different haplotypes.ResultsWe simulated reads from chromosome 6 exonic regions over a wide range of sequence divergence and coverage depth. We systematically assessed combinations between five mappers and five callers for their performance on simulated data and exome-seq data from NA12878, a well-studied individual in which multiple public call sets have been generated. Among those combinations, the number of known SNPs differed by about 5 % in the non-HLA regions of chromosome 6 but over 20 % in the HLA region. Notably, GSNAP mapping combined with GATK UnifiedGenotyper calling identified about 20 % more known SNPs than most existing methods without a noticeable loss of specificity, with 100 % sensitivity in three highly polymorphic HLA genes examined. Much larger differences were observed among these combinations in INDEL calling from both non-HLA and HLA regions. We obtained similar results with our internal exome-seq data from a cohort of chronic lymphocytic leukemia patients.ConclusionsWe have established a workflow enabling variant detection, with high sensitivity and specificity, over the full spectrum of divergence seen in the human genome. Comparing to public call sets from NA12878 has highlighted the overall superiority of GATK UnifiedGenotyper, followed by GATK HaplotypeCaller and SAMtools, in SNP calling, and of GATK HaplotypeCaller and Platypus in INDEL calling, particularly in regions of high sequence divergence such as the HLA region. GSNAP and Novoalign are the ideal mappers in combination with the above callers. We expect that the proposed workflow should be applicable to variant discovery in other highly divergent regions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3045-z) contains supplementary material, which is available to authorized users.
Highlights
Current variant discovery methods often start with the mapping of short reads to a reference genome; yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence
Method-specific single nucleotide polymorphism (SNP) calls in NA12878 We examined the known SNPs that were identified by GSNAP + Genome Analysis Toolkit (GATK) UnifiedGenotyper but missed in the public call set (Table 3), and those that were only present in the public call set (Table 4)
We have identified a few ideal mapper-caller combinations that are sensitive to both highly divergent regions and regions with low mutation rates, such as GSNAP + GATK UnifiedGenotyper in SNP calling and GSNAP + GATK HaplotypeCaller and GSNAP + Platypus in Insertion and deletion (INDEL) calling
Summary
Current variant discovery methods often start with the mapping of short reads to a reference genome; yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence. This is problematic for the human leukocyte antigen (HLA) region on chromosome 6p21.3. Compared to the hash-based mappers described below, the Burrows-Wheeler transform (BWT)based mappers like BWA are faster but tend to be less sensitive [11,12,13] They were developed for mapping reads to less divergent regions [11, 14]
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