Q1: 24675 (use grep -v '#' GAVIN-Plus_Demo_1000G_Spiked.vcf | wc -l)
Q2: 7 (to be sure, use grep -v '#' GAVIN-Plus_Demo_1000G_Spiked.vcf | cut -f1 | uniq)
Q3: 8 (use grep -v "#" GAVIN-Plus_Demo_1000G_Spiked.RVCF.firstpass.vcf | wc -l)
Q4: indels
Q5: 9 (use grep -v "#" GAVIN-Plus_Demo_1000G_Spiked.RVCF.vcf | wc -l)
Q6. rs113993990 (use diff GAVIN-Plus_Demo_1000G_Spiked.RVCF.firstpass.vcf GAVIN-Plus_Demo_1000G_Spiked.RVCF.vcf)
Q7. rs63750261
Q8. 50% (use grep 'rs63750261' GAVIN-Plus_Demo_1000G_Spiked.vcf to see original genotype)
Q9. epilepsy
Q10. 0.0378 (3.78%)
Q11. no
Q12. rs200307063 in DLD gene (see: https://www.umcg.nl/IDocuments/LAB-F024602E_UMCG_Conditions_and_genes_included_in_UMCG_preconception_screening_test.pdf)