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IndelRealigner -nWayOut: Possible to specify output directory?
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 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:
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.