How to annotate Missing Positions

Question

[abdallahamr5]

Hi :D

I am currently working on two file types that are missing positions of SNPs. ( genos_v2, and genetic_direction). I need to convert them to vcf formats. The VCF files are now missing the POS field. I tried using bcftools/ SnpSift to annotate the missing positions. But it seems that they are not made for that. I am using the reference file here ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/.

Any help is much appreciated! Thanks!

[Emily]

What information do you have?