Hi,

I would love to give your pipeline a try, however I have to admit I am having trouble figuring out the inputs for the demo. I tried the following command

perl ../bsa.pipeline.pl \
  -vcf pop.BSA.vcf \
  -pid R01,R02, \
  -bid R03,R04 \
  -bs 38 \
  -out Test_out 

I'm guessing on the parent and bulk names from the vcf file, but I don't what to put in the annotation field. Is it also required? also I have a VCF file with one parent and the two bulks. Is it possible to use this data with your pipeline?

Thanks in advance for your help