"I want to use GATK for genotyping and haplotype analysis. I have a VCF file from the 1001 Genomes Project (Arabidopsis thaliana) that I filtered using minor allele frequency. Now, I need to use GATK for haplotype analysis. My VCF file contains the following columns in the header: #CHROM, POS, ALT, REF, …, FORMAT, 88, 108 (accession codes).
Could someone guide me on how to perform this analysis on my dataset?"
Welcome, @puneet_gunwani
The only GATK tool currently hosted in Galaxy is GATK4 Mutect2. Link to the tool at the UseGalaxy.eu server.
We don’t have a Galaxy-specific tutorial for this one. Usage help is directly on the tool form, including links to the author resources and publications. The options will have both a short label and the original flag that would be used on the command line, so matching these up should be possible. Try to find an example from one of those resources that you want to replicate as a way to learn the baseline options – some simple examples are on the form, too.
If you want to try other tools, too, or are not sure of the manipulations possible, we do host tutorials, start here → Variant Analysis / Tutorial List. Browsing the tool panel will find more, try with the keyword “genotype”. Each tool usually has some basic help with links to more.
Hope this helps! 