Using PoolSNP to return non-SNP genotypes
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Entering edit mode
12 months ago
shpak.max ▴ 20

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
PoolSNP • 209 views
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