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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.
sorting a BAM file with PICARD
would you please advise: I am using PICARD in order to sort a BAM based on read name (it is a BAM file from EGA that contains cancer sequencing data), and when I do run PICARD SortSam, I am getting the following error (below), and the file does not get sorted. Is there a way i could fix it ? Thank you very much !
**Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 957453876, Read name HWI-ST7001002R:223:C14GPACXX:3:1305:7471:56486, MAPQ should be 0 for unmapped read"
The command from PICARD is :
**java -jar $PICARD SortSam \