we have a problem in our local galaxy instance (10392:1ae95b3aa98d release_2013.08.12) using bcftools (Version: 0.1.19-44428cd) from the tool shed to convert our bcf files into vcf. With bcf files less than ~ 3 GB everything works fine, but above that (we have a 13gb bcf file), the job gets stuck and is not terminating, neither successful nor with an error. Can somebody confirm this behavior?
Piping the Mpileup output directly into the bcftools using
Samtools mpileup -Duf "REFERENZ" "BAM_FILES" | bcftools view -cvg - > OUTPUT
at the command line works fine.
Trying to integrate this into the Mpileup wrapper failed so far.
Can somebody give us a hint how to solve this problem?
thanks in advance,
Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany -
Phone: ++49 ( 0 ) 3946 47 562 EMail: email@example.com:firstname.lastname@example.org