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When should I merge results from different lanes that are from the same sample?
I have 10 exome samples run on 5 lanes (each lane has 10 samples), so essentially I have 10 FASTQ files for each sample (Lane1_R1,2 ... Lane5_R1,2). My question is should I merge from the beginning (e.g. into Lane1-5_R1,2), or should I process these individually into BAM files and merge later? If the answer is the latter, then when and how should I merge the results? The aim of the project is to find mutations. Thanks.