Install the minorseq suite using bioconda, more info here.
The script is called mixdata.
Mixdata operates on BAM files. It mixes given BAM files at a given ratio and coverage. The first file is taken as the major clone, all following files are mixed in as minors with the provided percentage.
The mixdata script uses env variables for parametrization:
| Parameter | Description | Default |
|---|---|---|
COVERAGE |
The coverage of the final mixed BAM file. | 3000 |
PERCENTAGE |
The percentage of each minor clone. | 1 |
OUTPUT_PREFIX |
The output prefix of the generated file. | mix |
Mix three BAM files with 98/1/1% at 3000x:
$ ls
clone_1.bam clone_2.bam clone_3.bam
$ mixdata clone_*.bam
$ samtools view mix.bam | wc -l
3000
Equivalent call:
$ mixdata clone_1.bam clone_2.bam clone_3.bam
Mix five BAM files with
- 10% minors
clone_2.bamas major with 60%- 6000x coverage
- file name
insilico.bam
$ ls
clone_1.bam clone_2.bam clone_3.bam clone_4.bam clone_5.bam
$ COVERAGE=6000 PERCENTAGE=10 OUTPUT_PREFIX=insilico mixdata clone_{2,1,3,4,5}.bam
$ samtools view insilico.bam | wc -l
6000
Only dependency is samtools, which is part of the SMRT-bundle that is officially being provided by PacBio.