View Single Post
Old 09-27-2018, 05:01 PM   #6
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
Default

You could do some quality checks and remove duplicates and recalibrate; but if you are just starting off, just go ahead and assume the data is good and try and see if you can get a report on variations using a commonly used tool. After you get that working, you can check out the other stuff and re-run a new workflow. Order of importance would be : QC, duplicate removal or marking , then re calibration. Many here at work say recalibration is not worth the effort. Theoretically marking or removing duplicates may be important upstream to a variant caller, and again, theoretically a variant caller could do that work for you so read the docs for your tools and follow their advice.

Do try and run a QC tool on your fastqs early.
Absolute easiest QC on bam files is "samtools flagstat" (google it).
Study the results and see if you can make sense of them.
Richard Finney is offline   Reply With Quote