Variant Calling+Variant Filtering+ Variant Annotation

[Rokshan2016]

Hi, I am trying to use avocado for this operations - Variant Calling+Variant Filtering+ Variant Annotation. My data is in adam/sam/bam format. I did this operations

a.fastq data -->bwa alignment--> a.sam--> (transformalignments with sorting, mark dupicate, base recalibration)--> a. adam Now I want to do , Variant Calling+Variant Filtering+ Variant Annotation operations using Avocado and save it to .vcf

Any suggestion will be helpful

Thanks