I adjusted reference so that every entry started with "TRA" or "TRB", but it looks like the pipeline won't accept alignments to beta chain D segments. Is there a reason for this? Thanks!
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20:01:40, 2021-06-23 - TCRGO: Initialized logger, ready for TCRGO.
20:01:40 - INFO: Parsing input data...
20:01:40 - INFO: No index was detected, building index...
20:01:43 - INFO: Reading /cromwell_root/fc-d8b64044-a999-46bf-846b-b52b2a9a1b7c/e73b767d-850e-4ea6-bbec-55b73c343a62/TCRGO/0efbd8a7-a9e4-4130-bf5a-a60b0cb98451/call-alignment/out/pregnancy_test2_repairedsorted.bam...
20:01:43 - INFO: Reading CDR3 positions file and FASTA file...
20:01:43 - ERROR! TRBD1*01 could not be identified as 'V', 'J', or 'C' segment (got D as 4th character of reference name)
Related to #2 and #3:
I adjusted reference so that every entry started with "TRA" or "TRB", but it looks like the pipeline won't accept alignments to beta chain D segments. Is there a reason for this? Thanks!