Hi all,

We have recieved some bam files that were aligned to hg18. What would be the easiest workflow to get a VCF file from GATK in build hg19 ? We are running a local galaxy with only hg19 for the moment. Lifting the bam file would be my first choice, providing support to hg18 by generating all indices would be my last :-)


Best regards,

Geert



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