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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 \