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RealignerTargetCreator - lines without interval

I ran the GATK RealignerTargetCreator command and got an output file with some lines in non-interval format (about 6%).
For example: the line chrM:125-346 versus the line chrM:7684
When I ran the next IndelRealigner command it failed with the following error message, indicating the line without interval:
"##### ERROR MESSAGE: Invalid argument value 'targetIntervals' at position 10.

ERROR Invalid argument value 'GRC13283077_var_list' at position 11."

What is the reason for this output? What can I do about it?
Please advice.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @Lily,

    Actually chrM:7684 is a valid interval. Your problem is probably a typo in your command line, as the "invalid argument value" error occurs when the command is being parsed, not during execution. Can you please post your complete command line?

  • LilyLily Member
    edited March 2014

    Thanks for the very prompt reply. You were right, it was just a typo... Thanks!!
    I hope it is OK that I'll take this opportunity to ask one more question:
    In the log followed the RealignerTargetCreator, I got the following messages:

    INFO  15:14:53,687 TraversalEngine - Total runtime 6209.96 secs, 103.50 min, 1.72 hours 
    INFO  15:14:53,688 TraversalEngine - 32488016 reads were filtered out during traversal out of 102958833 total (31.55%) 
    INFO  15:14:53,689 TraversalEngine -   -> 385 reads (0.00% of total) failing BadCigarFilter 
    INFO  15:14:53,689 TraversalEngine -   -> 29719 reads (0.03% of total) failing BadMateFilter 
    INFO  15:14:53,690 TraversalEngine -   -> 19400550 reads (18.84% of total) failing DuplicateReadFilter 
    INFO  15:14:53,690 TraversalEngine -   -> 13057352 reads (12.68% of total) failing MappingQualityZeroFilter 
    INFO  15:14:53,691 TraversalEngine -   -> 10 reads (0.00% of total) failing UnmappedReadFilter

    Are these percentages reasonable?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    No problem. The numbers you're getting for DuplicateReadFilter and MappingQualityZeroFilter are rather high. This is not unusual, but the Broad's Genomics Platform labs have put a lot of effort into developing procedures that minimize wasted sequence, so we typically see much lower numbers. You may want to discuss this with whoever produced the sequence data.

  • LilyLily Member
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