Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs
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...As previously reported [147], we noted that false positive variant calls within intronic and intergenic regions were the most common consequence of dephasing in low complexity, pyrimidine-enriched intervals....
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...3’ SSs and SRFBSs), it may prove essential to adopt or develop alignment software that explicitly and correctly identifies variants in these regions [147]....
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...Intronic and intergenic variants proximate to low complexity sequences tend to generate false positive variants due to ambiguous alignment, a well known technical issue in short read sequence analysis [146, 147], contributing to this discrepancy....
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...Alternatively, it is possible to study their variability directly from the NGS whole genome sequence, once the reads are mapped to a reference genome (Fondon et al. 2012; Gymrek et al. 2012; Tae et al. 2014; Ummat & Bashir 2014)....
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...The theoretical distribution we have chosen derives from (Tae et al. 2014)....
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...For example, as the intensities add up, when the two alleles of an heterozygote have similar length, the resulting distribution can show one single mode which would inevitably lead to a false assignment (Tae et al. 2014)....
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"Discretized Gaussian mixture for ge..." refers methods in this paper
...The reads were aligned to the human genome reference NCBI build 37 by BWA and realigned by GATK....
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...The performance of genotyping programs were compared for different mapping results generated by two different mapping programs, BWA and Novoalign (http://novocraft.com)....
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...After BWA mapping and GATK realignment, microsatellite loci satisfying the following three conditions were chosen for the comparison....
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...To create the input for GenoTan, BWA (Li and Durbin, 2009) and GATK were used to map the sequence reads to the reference and to realign the reads, respectively....
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...GATK, DIndel, GenoTan and RepeatSeq had correct percentages of 79.8%, 92.4%, 91.8% and 53.7% with BWA mapping, respectively, and 84.3%, 95.6%, 95.4% and 55.0% with Novoalign mapping....
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"Discretized Gaussian mixture for ge..." refers methods in this paper
...To create a list of microsatellite loci, TRF (Benson, 1999) was used to search repeat sequences including incomplete repeat sets....
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...For users who want to use TRF (Benson 1999), an additional PERL script to convert the TRF results to the microsatellite list is available in our software package....
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