Perhaps we need to unnormalise with -m +any each individual file before merging in order to avoid duplicate records? I can try this: for each component VCF: bcftools norm -m +any then bcftools merge -m none bcftools norm -m -any And check for duplicate CHROM, POS, REF, ALT I will ...
// norm and create plots for (i=0; i<args->nfold; i++) { som_norm_counts(args->som[i]); if ( args->prefix ) { char *bname = msprintf("%s.som.%d", args->prefix,i); som_create_plot(args->som[i], bname); free(bname);...