I have some moderately degraded DNA (DIN < 6) which will be used for standard library prep followed by illumina paired end sequencing. I was wondering what would be the consequences of degraded material with regard to downstream analyses such as SNP calling, structural variant detection etc.
I have been working with RNA preps where degraded mRNA would cause a 5' bias in resulting library when using polyA capture approach. So degraded RNA matters. Is there any such effects on degraded DNA? Long strand DNA will have to sheared anyway during library prep to some shorter insert sizes. So does it even matter that I start with degraded DNA?