In the tool command line template, you can do this: ${input_bam.metadata.bam_index} to get the the location of the bai. See the FreeBayes wrapper for an example. Best, J. On Jun 29, 2012, at 10:03 AM, Geert Vandeweyer wrote:
Hi,
I'm working on a tool that will export vcf files together with bam/bai files to a long term storage location on our local installation. How can i get the path to the automatically created bai file for a provided bam file? Can it be derived from the file bam file path?
Best regards,
Geert Vandeweyer
--
Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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