I am trying to use ANGSD to call SNPs. I succeeded in using the allele frequency estimation methods that rely on genotype likelihoods, but am I correct in concluding that it doesn't support SNP calling using the allele frequency estimation method directly from base counts (-doMaf 8)? I can run this successfully:

./angsd -out PairedPlus_all_counts -doMajorMinor 2 -doMaf 8 -bam pairedplus_dupes_bam.filelist -doCounts 1 -P 5

but once I add "-SNP_pval 1e-6", I get the error: Segmentation fault (core dumped)

Thanks for the help!