aln2variants

This example container uses Freebayes to call variants from a sorted BAM/CRAM file with reads aligned against H37Rv ASM19595v2. In addition to the aligned reads, it also expects a CSV with target variants for which there must be a genotype in the output file. This is needed for prediction containers relying on a pre-determined set of variants as input data. The header line of the CSV should be POS,REF,ALT,AF with the AF column holding allele frequencies that can be used to replace non-calls.

It will write the called variants to a CSV with the columns POS,REF,ALT,GT.

Usage

The container uses /data as working directory and will create the output file there. It can be called like this:

docker run -v $PWD:/data \
    julibeg/tb-ml-variants-from-aligned-reads:v0.4.0 \
    -b aligned-reads.bam \
    -t target-vars.csv \
    -o called-variants.csv