So U Found A Mutation?
Project description
Found a mutation in one or more samples? Now you want to check if they are in another sample. Unfortunately mutect, varscan or whatever other variant caller is not calling them. Use SUFAM. The super sensitive validation caller that calls everything on a given position. All you need is a vcf with the mutations that you are interested in and the sam/bam file of the sample where you want to find the same inconsipicuous mutation.
Installation
pip install sufam
Run
usage: sufam [-h] [--sample_name SAMPLE_NAME] [--format {matrix,sufam}] reffa vcf bam positional arguments: reffa Reference genome (fasta) vcf VCF with mutations to be validated bam BAM to find mutations in optional arguments: -h, --help show this help message and exit --sample_name SAMPLE_NAME Set name of sample, used in output. --format {matrix,sufam} Set output format
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