If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
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?