I know that PoolSNP is optimized for variant calling, but surely there's some way to get to to return a vcf with allele frequency counts at all sites rather than just the SNPs, as can be done with GATK. Is there something I need to do other than set min-count to 0? I think that the poolsnp.py code contains various checks to determine whether there is more than a single allele, but it's not immediately clear to me if there's a simple modification that would return genotypes at all sites with mind-cov greater than the set threshold.
I also tried commenting out lines 203-204 in PoolSNP.py with the conditional
if len(totalalleles) < 2: continue
This changed nothing, I'm still not getting 0/0 or 1/1 sites in the vcf
The commands I used to execute PoolSNP are appended below:
$pool_snp_path/PoolSNP.sh mpileup=$sample_path/SRR_Realign_AllFiles.mpileup reference=$ref_path/DmelRef.fasta names=$names max-cov=0.98 min-cov=5 min-count=0 min-freq=0 miss-frac=0.5 jobs=0 BS=0 output=$out_path/All_Files_SRR_SNP_AllSites