Sentence examples for read realignment from inspiring English sources

Therefore, split read realignment without using BWT is necessary to allow reads to be globally mapped.

Next, to help with indel identification later in the pipeline, read realignment was performed around indels.

The ABRA algorithm consists of localized region assembly, contig building, alignment of assembled contigs and read realignment.

Soft-clipped read realignment can theoretically find deletions of any size, but it has limited power to detect insertions owing to the short read length of current sequencing technologies.

BAM files generated from the previous reference genome-based raw read realignment step were then processed according to the guidelines of GATK's BestPractice version 3.3 for downstream analysis (https://www.broadinstitute.org/gatk/guide/best-practices, last accessed August 2015).

Such read realignment has potential implications for genotyping known SVs in newly sequenced individuals, and/or discovering de novo SVs within loci that are known or expected to have a strong copy-number association with genetic diseases (McCarroll and Altshuler, 2007).

Removal of duplicated reads, realignment of reads around insertion and deletions were performed as previously described [ 21].

Briefly, this consisted of flagging duplicate reads, realignment around indels, base recalibration and variant calling on all trios simultaneously using the HaplotypeCaller tool.

The assembly metrics showed the smaller number of contigs (262,747 vs 278,792), shorter genome length (by 0.2 Gbp), more genes predicted (by 2,426), but similar proportion of repeat elements and raw reads realignment rate (approximately 91% on average) compared to the previous version of genome assembly.

BAM sorting, duplicate read marking, realignment, base quality recalibration, variant calling and filtering were performed with the same parameters used for the bwa-GATK variant calling pipeline in Proton reads.

Picard (http://picard.sourceforge.net/, last accessed February 9 , 2015 was used to mark duplicated reads, and realignment of reads was performed in GATK v2.3 (McKenna et al. 2010).