Hello,

Recently I've tried to use ART simulator to create some reads for further analysis. I've used the next command to do so (I am using chr20 of hg19 reference genome):

art_illumina -sam -i hg19_chr20.fa -p -l 100 -ss HS25 -f 10 -m 200 -s 10 -o test

After converting the sam file to bam, sorting and indexing it, I've used ANGSD software to calculate the proportion of heterozygous genotypes (as described here) , that turned out to be extremely low (1e-9)

Am I missing some option in ART that can handle this, or is it because I am using chromosome 20 of hg19 as input sequence? (I've tried to use the whole reference genome as an input for ART and obtained better results (1e-6), however it's still not realistic) Can it be the way ANGSD produces genotype likelihood files?