Sentence examples for realigned file from inspiring English sources

The Bambino program (Edmonson et al. 2011) was used to process the realigned file and detect the indels within it.

ABRA accepts BAM files as input and outputs realigned BAM files, allowing flexibility in downstream analysis.

To further increase the local realignment accuracy, after local realignment, we performed base quality score recalibration on the realigned BAM files using GATK's recalibration tool.

The realigned SAM files were used for variant calling using a recently developed statistical algorithm called CRISP that uses information from aligned sequence reads within each pool as well as across all pools.

The locally realigned BAM files were used to detect CNV.

Realigned BAM files were subjected to base quality recalibration using BaseRecalibrator from the GATK and the recalibration report for each realigned BAM file was generated using default setting for covariates and dbSNP build 133 as a variant database for known sites.

The following post-processing was applied to the BAM files: reads in the BAM files were realigned with Realigner Target Creator and Indel Realigner in the Genome Analysis Tookit 2.5-2 (Gand), and their base quality scores were recalibrated with Base Recalibrator and Print Reads in GATK [ 40, 41].

We identified small insertions and deletions on the realigned, recalibrated pileup files (aligned to the N16961 reference genome) using Varscan, requiring a 75% variant frequency.

These realigned and recalibrated BAM files were then used to determine SNVs and CNVs.

Next, using GATK (V2.4-9) [ 2], the initial BAM files were realigned and the base quality scores were recalibrated.

The resulting PE bam files were realigned using GATK IndelRealigner and single nucleotide variant (SNV) and indel calling was performed with the GATK Unified Genotyper (.vcf output) implemented in our Galaxy pipeline.