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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:

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,


Best Answer


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