I'm trying to use picard tool set up with Conda, however, it doesn't work with any VCF i'm throwing at it, e.g. this VCF file throws an error to simple filtering command:
picard FilterVcf MIN_DP=10 I=trio.2010_06.ychr.sites.vcf.gz O=testt.vcf
Exception in thread "main" picard.PicardException: The input vcf must have a sequence dictionary in order to create indexed vcf or bcfs. at picard.vcf.filter.FilterVcf.doWork(FilterVcf.java:106) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Although test VCF is fine and work with other tools with no issue.
Is there an accepted workflow to prepare VCF files for work with picard? Or is there some other obvious issue i'm ignoring?
I also can't find any tutorial with test data to confirm if my system has everything set up correctly.