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.

SortSam in GATK4.0.1 fails, Picard 2.11 SortSam works on the same file

I try to use the standard workflow sequence with GATK4 as it was published in the tutorials last year for Picard/GATK combination. I called the SortSam tool as follows:
./gatk --java-options "-Xmx4G" SortSam -I:filename].sam -O:[filename]_Sorted.bam -SO:coordinate

and GATK4 4.0.1 returned the following error:
"No value found for tagged argument: I:[filename].sam
Tool returned:
1"

The tool itself shows usage example by picard invocation with its native syntax (I= instead of -I:).
Using picard 2.11-snapshot on the same sam file produces a normal sorted BAM file.
Is this a bug or I did something wrong?

Thank you,

Lev

Best Answer

Answers

Sign In or Register to comment.