Dear all,
would you please advise: beside SAMTOOLS, PICARD or SAMBAMBA, is there any tool that you would recommend 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. Thanks !
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
Thank you Philipp for your suggestion !