Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF view tool in galaxy is supposed to convert mpileup's BCF variants file to VCF variants file, but unfortunately does not change the binary encoding. I am attempting to call variants for two drosophila samples against the latest dm6 reference, but other variant callers do not seem to offer the same version reference genome as an index file or do not have the option to output genotypes. I am specifically interested in determining homozygous vs heterozygous variant sites. Any suggestions on variant callers that are fit for this specific task would be greatly appreciated.
The reference genome dm6 should be indexed for most variant callers at Galaxy Main http://usegalaxy.org.
GATK is one exception and those tools are deprecated. GEMINI is also a noted exception; at Galaxy Main http://usegalaxy.org, only hg19 is indexed/supported.
If the tool you want to use does (not including GATK or GEMINI) do not have dm6 indexed - please comment back about which tool so we can address that if possible. Meanwhile, a custom reference genome can be used with nearly all other tools if needed, this is how: https://galaxyproject.org/learn/custom-genomes/
As an alternative, pileup format (instead of VCF) can be directly given to Varscan to compute the consensus genotype. After, tools in the group VCF Manipulation can be used to further analyze those results. Or you can use Freebayes in one step (input the mapped BAM data to produce a VCF with genotype information).
Thanks, Jen, Galaxy team