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sort samtools sort -o sorted_out unsorted_in.bam. Read the specified unsorted_in.bam as input, sort it by aligned read position, and write it out to sorted_out. Type of output can be either sam, bam, or cram, and will be determined automatically by sorted_out's file-extension. samtools sort -m 5000000 unsorted_in.bam sorted_out
The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects.
SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present. Headings begin with the '@' symbol, which distinguishes them from the alignment section. Alignment sections have 11 mandatory fields, as well as a variable number of optional fields. [1]
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Variant calling in RNA-Seq is similar to DNA variant calling and often employs the same tools (including SAMtools mpileup [134] and GATK HaplotypeCaller [135]) with adjustments to account for splicing.
The pipeline employs tools like Bowtie, TopHat, ArrayExpressHTS and SAMtools. Also, edgeR or DESeq to perform differential expression. MultiDE; Myrna is a pipeline tool that runs in a cloud environment (Elastic MapReduce) or in a unique computer for estimating differential gene expression in RNA-Seq datasets. Bowtie is employed for short read ...