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MergeBamAlignment – Select primary alignment
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?