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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

    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

    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.

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