bioinfoipec/samtools repository overview

⁠SAMtools

This image facilitates the usage of:

• SAMtools⁠: tool for manipulating next-generation sequencing data.
• htslib⁠: is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools.
• BCFtools⁠: contains all the vcf* commands.

To see SAMtools options, just run: docker run --rm bioinfoipec/samtools samtools --help or docker run --rm bioinfoipec/samtools bcftools --help.

⁠Using the SAMtools image

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data bioinfoipec/samtools <samtools_or_bcftools> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <samtools_or_bcftools> to the name of either SAMtools or BCFtools executable you want to use.
• <options> with the specific options of the SAMtools or BCFtools application. These options will include the input/output files, which should be referenced under /data/.

For instance, if you want to generate a high quality VCF file from an input SAM file, you should run the following three steps:

• docker run --rm -v /your/data/dir:/data bioinfoipec/samtools samtools view -bS /data/aln-pe.sam > aln-pe.bam

• docker run --rm -v /your/data/dir:/data bioinfoipec/samtools bash -c "samtools mpileup -uf /data/chr19_KI270866v1_alt.fasta /data/aln-pe.bam | bcftools call -mv > /data/var.raw.vcf"

• docker run --rm -v /your/data/dir:/data bioinfoipec/samtools bash -c "bcftools filter -s LowQual -e '%QUAL<20 || DP>100' /data/var.raw.vcf > /data/var.flt.vcf"

⁠Test data

To test the previous commands, the input SAM file and the input FASTA file are available in testdata directory.