how to visually compare BAM file differences
I am a Bioinformatics novice learning workflow of calling somatic mutation . I found actions related to BAM file are these :
sort, markdup ,reorder ,indel realignment,BQSR , I want to known the differences of them after I execute one step .
in fact ,I'm a little confused ,GATK 3 and GATK 4 are somewhat different, There are also many software similar to GATK, I don't know the necessity of each step, maybe there will be a better way to learn, thank you for all your help
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