Attention:
The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

fastqtosam --USE_SEQUENTIAL_FASTQS

Hi,

I am starting the GATK workflow on several hundred exomes working with fastq.gz files. I am using fastqToSam in Picard to convert my fastq files (paired end) to uBAM. This works fine on one set of files but I have many hundred to process. It looks like --USE_SEQUENTIAL_FASTQS will help me, but I can't find documentation on syntax beyond the fact that it is boolean. Can you tell me how I need to specify files to make this work? Is there any way that I can use a wildcard and provide a directory of fastq files? I'm wondering what a typical workflow is for processing hundreds of samples.

Thanks,
Nancy

Best Answer

Answers

Sign In or Register to comment.