Hi again guys!
So this time with a new question. I have a list of variant calls (basically, SNPs) for a mouse genome sample. SNP positions are reported using the reference mouse genome sequence. What I would like to do is to take this list and substitute each reported SNP position on the corresponding reference mouse genome sequence as to obtain my own "genome" with the corresponding SNPs. However, I don't know how to do this task in an efficient manner just using my current programming skills.
I was thinking on storing each bp as part of an array, and then reading my SNPs file and then changing, but wouldn't storing a whole chromosome sequence be too much?
I'd like to know if you know of any other better way :)
This sounds great, will check it out.
couldn't access the python script, can you make it available again? thanks