I would like to convert a bam file (thas has been generated following GATK Best Practices - Data pre-processing for variant discovery) to initial fastq files (R1 and R2).
I thought I could use SamToFastq Picard's tool.
I did not find any pipeline with "SamToFastq" in the Best Practices. So I just wanted to be sure that I can use SamToFastq and only that (in other words, that no additional step is needed to retrieve fastq files able to enter a new pre-processing pipeline).
Thanks in advance for you help!
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