My lab is working on an exome-seq pipeline and I have been given the bam files after performing Indel realignment. I want to perform again all the pipeline as sanity check.
I have converted the bam files to fastq using Picard SamtoFastq and when performing the quality control of the fastq files, the plots are not the same, in spite of being similar. Also I am missing 5 millions of reads in respect to the initial fastq files.
Is there way to get the initial fastq files from this Indel Realigned files?
Thanks for reading,