IndelRealigner -nWayOut: Possible to specify output directory?

teamcoopteamcoop Ontario, CanadaMember

I'm putting together an in-house pipeline for processing of paired tumor-normal BAMs. I've set it up to make a single intervals file for each pair and then want to have separate BAMs for BQSR, so I thought I'd use IndelRealigner with -nWayOut. However, the realigned BAMs are output to whatever directory I've run the script from, rather than the same directory as the BAM files I provided to -I.

I tried to create a .map file with full pathnames to both the input and output files, but received the error:

##### ERROR MESSAGE: Bad input: Input-output bam filename map does not contain an entry for the input file 3528.dedup.bam

The corresponding entry in the .map file had the format:

/users/home/project/cocleaned/3528.dedup.bam /users/home/project/cocleaned/3528.realigned.bam

Is there a way to specify an output directory in conjunction with -nWayOut? If not, I can probably hackishly search for the realigned files, but I thought I'd check.

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Have you tried using just the filename instead of the full file path for the input field in the map file? Based on the error message I think that's what the program is looking for internally.

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