How to include each steps in the bam header

Question

[ifudontmind_plzz]

Hi,

I'm doing sequence analysis (starting from alignment of fastq to BaseRecalibrator). I would like to know if there is any by which we can include each steps in the bam header.

Answer 1

[Ashutosh Pandey]

Almost all aligners add the alignment command used in the bam header under the @PG tag. Picard also adds such information in the bam header if you use it for the post processing of your sam/bam file. Even if you use a program that doesn't add such information under the @PG tag, you can edit the header on your own. Search for edit bam header in this forum and here is the reference for things you will have to take care while adding a info into the header. All these info will will go under the @PG tag. https://samtools.github.io/hts-specs/SAMv1.pdf