I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads QC FASTQ Groomer FASTQ Trimmer
Convert to Fastqsanger file
Map to reference (Map with BWA for Illumina)
Convert SAM file to BAM
Mark to Duplicates (Picard tools) or make a VCF file.
Analysis by GATK tools such as: Indel realignment, Base Recalibration, Variant Calling, variant Filtering, annotation (SnpEff)
I have a problem at step 5 , I don't know how to do. Would you like help me, please.