Sentence examples similar to alignment map from from inspiring English sources
The sequence alignment map output from BWA was sorted and indexed to produce a binary alignment map (BAM) using Samtools 0.1.18 [ 23].
A final VCF file was derived using GATK software (https://www.broadinstitute.org/gatk/) that contained genotypes at all positions for all samples using the list of nonredundant SNP positions, binary alignment map (BAM) files exported from CLC Workbench for each individual sample, and BES FASTA file.
Alignments were converted from sequence alignment map (SAM) format to sorted, indexed binary alignment map (BAM) files (SAMtools version 0.1.18; http://sourceforge.net).net
Conversion from sequence alignment map format to sorted, indexed BAM files was done using SAMtools (version 0.1.18 [ 9]).
The mapped reads were extracted from the sequence alignment map and converted into a base space fastq format using SamToFastq.jar from Picard tools (version 1.113; http://picard.sourceforge.net).net
Alignments were converted from the sequence alignment map (SAM) to binary alignment map (BAM) format.
Alignments were converted from the sequence alignment map (SAM) format to binary alignment map (BAM), and the BAM files were sorted and indexed using SAMtools (version 0.1.19).
Orphaned reads (mate of reads whose one end mapped to transgene) from name sorted sequence alignment map (SAM) [ 23] file were then extracted using custom Perl scripts.
This was used in combination with a binary alignment map (BAM) file generated by mapping the unmapped mates from the plasmid to the PH-1 reference.
For this study, the binary alignment mapped (BAM) files generated from the study of Ahmad et al. [ 25] were used to generate Simple Alignment Map (SAM) and, subsequently, Variant Filter Calling (VCF) files through the use the routine mpileup in the software SAMtools [ 90].
These programs are specifically designed to identify genomic structural variations through sliding window and clustering strategies by processing sorted binary alignment mapped or SAM files resulting from the alignment of sequences from 'Indo' and 'Su Shuai' to the 'Golden Delicious' reference genome.
