I exactly followed the below galaxy workflow that contain targetted re-sequencing data for a father mother and child trio.
https://usegalaxy.org/u/coursera/p/genomic-data-science-with-galaxyidentify-polymorphic-sites
I was successful in creating all the steps till the end in my galaxy. However, from the variant call format file or galaxy workflow
How many SNPs are there in all three individuals? How to count How do I extract SNPs – single nucleotide variants, insertion/deletion variants, multi-nucleotide variants from the VCF file in all three individuals? How to download variant call format file from galaxy workflow?
I am very new to this field. Please be kind and let me know how to look in the steps of the workflow. I appreciate your time and thank you very much in advance.
