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Samtools sort sample.bam -o Now let’s check the order: samtools view | head Notice anything different about the coordinates of the alignments? Samtools “index” Indexing a genome sorted BAM file allows one to quickly extract alignments overlapping particular genomic regions. That is, ordered positionally based upon their alignment coordinates on each chromosome. It must be sorted such that the alignments occur in “genome order”. Samtools view sample.bam| head Doing anything meaningful such as calling variants or visualizing alignments in IGV) requires that the BAM is further manipulated. In other words, the BAM file is in the order that the sequences occurred in the input FASTQ files. Samtools view sample.bam| head samtools “sort” When you align FASTQ files with all current sequence aligners, the alignments produced are in random order with respect to their position in the reference genome. Samtools view -S -b sample.sam > sample.bam Now, we can use the samtools view command to convert the BAM to SAM so we mere mortals can read it. Samtools follows the UNIX convention of sending its output to the UNIX STDOUT, so we need to use a redirect operator (“>”) to create a BAM file from the output. We must also say that we want the output to be BAM (by default it produces BAM) with the -b option. We must specify that our input is in SAM format (by default it expects BAM) using the -S option. To convert SAM to BAM, we use the samtools view command. However, it is consequently very difficult for humans to read. The binary format is much easier for computer programs to work with.
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Examples: samtools view samtools sort samtools depth Converting SAM to BAM with samtools “view” To do anything meaningful with alignment data from BWA or other aligners (which produce text-based SAM output), we need to first convert the SAM to its binary counterpart, BAM format.
Download samtools download#
Cd samtools-demo Download the example gzipped SAM file I have provided.Ĭurl > gzip -d The samtools help To bring up the help, just type samtools As you can see, there are multiple “subcommands” and for samtools to work you must tell it which subcommand you want to use. Cd ~ mkdir samtools-demo Navigate into that directory. You may already have a src directory mkdir src cd ~/src git clone git clone cd samtools make cp samtools ~/bin Setup Create a new directory from your home directory called “samtools-demo”. Installing samtools Follow these steps: cd ~ # optional.
Download samtools how to#
Synopsis Our goal is to work through examples that demonstrate how to explore, process and manipulate SAM and BAM files with the samtools software package. Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools: Reading/writing BCF2/VCF/gVCF files. See also release notes for samtools, bcftools, and htslib. Download current source releases: samtools-1.9 bcftools-1.9 htslib-1.9.