MergeBamAlignment – Select primary alignment

micknudsen

Hi,

In the current best practices workflow gatk4-data-processing, you recommend using uBAMs instead of FASTQ files. Great idea! However, when it comes to merging with the BWA alignment BAM, there is something that puzzles me.

Here is an example of a paired-end read mapped by BWA:

XXXXXXXX:412:YYYYYYYYY:1:11101:10001:10497  83  chr16   1229894 0   149M    =   1229833 -210    GGGCCGCGTAGGCGCGGCTCGCCAGGACGGGCAGCGCCAGCAGCAGCAGATTCAGCATCTGGGGAGCAAGGAGGAGCATCGTGGGCCTGGCCGGGCCTCACAGGGCAGGGCTGGGGGCTACAGATTGTGGGGTGAAGAATGGAGCTGAG   AAAAA/E<EEAA</A/<EA<<EEEEEEEE/EEEAAEEAEE/EAEAAEEEEEEEEEEEAEEAAEEAEAEAAEEEEEEEEEEEEAAEEEEAE6EAEEEEEEEE/EEEEEEE/EE/AEAAEEEEEEEEEAAEEEEEEEEEEEEEEEEAAAAA   XA:Z:chr16,+1240848,149M,1;chr16,+1256211,149M,6;   MC:Z:150M   MD:Z:147G1  RG:Z:NS500158.1 NM:i:1  AS:i:147    XS:i:147
XXXXXXXX:412:YYYYYYYYY:1:11101:10001:10497  163 chr16   1229833 0   150M    =   1229894 210 CCAGGCCCTGACCTGTGGAATGTGGTGAGGGGCAGGGTGGACCCCGGCTGGGACTCACCAGGGGCCGCGTAGGCGCGGCTCGCCAGGACGGGCAGCGCCAGCAGCAGCAGATTCAGCATCTGGGGAGCAAGGAGGAGCATCGTGGGCCTG  AAAAAEEEEEEEEEEEEAE6EEEAEEEEEEEEEEEEEEAE/EEEEEEEEEEA/AEAEEEEEEEEEAEAE<EEE6A/EEAAAEEEA/EEAAEEAEEE/AAAAEEEEEEEAE/EEEEEEEEEEAEEEEEEAEEEAEE6EAEEAE<</AAA<6  XA:Z:chr16,-1240908,150M,0; MC:Z:149M   MD:Z:150    RG:Z:NS500158.1 NM:i:0  AS:i:150    XS:i:150

Note that BWA has suggested an alternative alignment given in the XA tag. When using MergeBamAlignment as in the best practices pipeline, the alignment in XA is chosen. I have tried modifying the --PRIMARY_ALIGNMENT_STRATEGY parameter, but is doesn't change anything.

In the old days before uMAPs, you worked directly with FASTQ files and hence used the primary alignment selected by BWA. What is the motivation for changing that?