This might be a newbie question, I'm a QM Chemist stepping in for a bioinformatician at work, so I am sorry in advance for the lack of necessary information required to help with my question.
I have a documented number of steps to follow that allows me to align my paired-end reads to a human reference genome and then perform variant calling. I am using Samtools, GATK and Picard. I am also using the same reference gnome fa file as my colleague.
However, when I perform the variant calling and I look inside the sam file I generated, I only have reference names "ref|NT_.....|". The original files generated by the bioinformatician have "NC...." as reference names. The code further down the pipeline will require the NC... naming structure.
I don't want this question to feel too much like a black box, but if I could get a general idea of what will have caused the difference in read reference names, I would be really grateful and I can go from there.