pegi3s/freebayes repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of FreeBayes⁠, a variant calling program.

⁠Using the FreeBayes image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/freebayes -f reference.fa /data/input.bam

For mtDNA data make sure you use the -p 1 and --pooled-continuous options:

docker run --rm -v /your/data/dir:/data pegi3s/freebayes -f rCRS.fasta -p 1 --pooled-continuous /data/input.bam

To get the result in vcf use the -v option:

docker run --rm -v /your/data/dir:/data pegi3s/freebayes -f rCRS.fasta -p 1 --pooled-continuous /data/input.bam -v data/output.vcf

In either of these commands, you should replace:

• /your/data/dir to point to the directory that contains the BAM file you want to analyze.
• input.bam to the actual name of your input file.
• reference.fa to the actual name of your reference file (rCRS.fasta is included with the docker image).
• output.vcf to the desired name of the output file.

To see the freebayes help, just run docker run --rm pegi3s/freebayes --help.