Hi I have a sam file. The 5th column of the sam file tells us the quality score. In my sam alignment file there are reads which have quality score of 2. I would like to remove them from my sam file because i think these reads which have a low quality score are not that important in my analysis. I want to keep the headers of sam file too.
Any code or unix one liner would be appreciated.
Thanks for the help
Is it not possible get rid of the chaining for the quality filtering?
I tried the code in a jiffy, and for sure missed a parameter, so had to put the pipe. Of course, it works, I'll edit again :)
thnks sukhdeep works smoothly cheers
No worries, could you also edit the question to something like Filtering a Sam file for quality scores Cheers