This function transforms a BAM file into a text file. Specifically, this function uses samtools mpileup to translate your BAM into a tab-separated file. We then filter this file to remove indels and deletions. When running this function, a temporary folder will be created (named 'temp/'), however this folder will be removed once the process is complete.
Arguments
- name
File name without the suffix. For example, if your file is called "frog.bam", this input should be "frog".
- inpath
Location of input file.
- outpath
Location for output file.
Details
Warning, due to the processing time needed for samtools mpileup, this step may take some time. This function also requires samtools to be located locally. Please see our Data Preparation article for more information. Warning, this writes a temporary folder titled 'temp'. If you want to run multiple samples at once, we suggest you set the working directory to separate locations to ensure that your temp folder/files are not overwritten.