# coverage alignment depth and percent coverage # import Converts FASTA or FASTQ files to SAM/BAM/CRAM # quickcheck quickly check if SAM/BAM/CRAM file appears intact # collate shuffle and group alignments by name # ampliconclip clip oligos from the end of reads # targetcut cut fosmid regions (for fosmid pool only) # calmd recalculate MD/NM tags and '=' bases # Program: samtools (Tools for alignments in the SAM format)
help, all the available utilities are listed: samtools -help If you run samtools on the terminal without any parameters or with
#Bam file format example install
Once you have installed Miniconda, you can install SAMtools as follows: conda install -c bioconda samtools For example: # clone this repoĭocker run -rm -it -v $(pwd):/work davetang/r_build:4.1.0 /bin/bashįor installing SAMtools, I recommend using Conda and the BiocondaĪnaconda because Anaconda comes with a lot of tools/packages that you Script if you want to generate this file yourself, please use thisĪnd the Makefile in this directory. This README is generated using the create_readme.sh (stored in the eg folder) generated as per The examples in this README use the ERR188273_chrX.bam BAM file Latest information on SAMtools, please refer to the release High-throughput sequencing data, at some point you will probably have toĭeal with SAM/BAM files, so familiarise yourself with them! For the The SAM (Sequence Alignment/Map) format (BAM is just theīinary form of SAM) is currently the de facto standard for storing SAMtools provides various (sub)tools for manipulating alignments in the
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