Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to read a SAM record into the SAMRecord class
I am trying to read in Array[htsjdk.samtools.SAMRecord] into the SAMRecord class and trying to get their starting position by the getAlignmentStart method of the class. I have created the SAMRecord object like this (in Scala):
// samRecordInput is an array of type Array[htsjdk.samtools.SAMRecord]
val header = new SAMFileHeader()
val samRecord = new SAMRecord(header)
How can I pass this array to the samRecord object?