How to anonymise a bam file I have a bam file of, for instance, RNA-Seq, which contains patient-identifiable data in the form of Single Nucleotide Polymorphisms (SNPs) throughout.
I would like a technique to take this aligned bam file and replace all the non-reference bases with the reference bases at the equivalent positions (hard-clipping any soft-clipped bases while doing so), in order to have an anonymised bam file without the patient-identifiable information.
What is the best way to do this? I want the resulting anonymised bam file to have the reads in the same positions, for downstream tools that care about the alignment positions.
You can simply replace the sequence and quality scores with a single * in each field. The CIGAR information will still be there, so it will be apparent where there were InDels and possibly mismatches (assuming your aligning uses = and X CIGAR operations), but since the actual sequence of these variants cannot be known this is quite anonymized.