MG-NIPD contains 3 different scripts to perform prenatal diagnostics, one script each for CFTR, CYP21A2 and HBB. The scripts require as input: Haplotypes optained in each parent, as generated by Haplotyper1.5, or an alternative, the format is coordinate:allele Example: 5536852:A
vcf files obtained from the TLA .bam files using samtools command: "samtools mpileup -AuDIB " and converted to vcf using Bcftools: "bcftools view -H -G"
vcf files obtained from mapped and processed cfDNA and CVS DNA(if available) using the same samtools commands "samtools mpileup -AuDIB " "bcftools view -H -G"