Hi, I am leaning from the ‘‘Exome sequencing data analysis’’ tutorial in order the develop the skill to analyze my genomics data against the reference genome for identifying variants on the specific genes of my samples.
I followed the tutorial to use the ‘‘SnpSift Annotate’’ to give variant ID to the vcf file of the ‘‘father’’.
However, the dbSNP vcf file (dbSNP_138.hg19.vcf) offered in the tutorial does not contain ID information.
So I could run SnpSift Annotate, but the output vcf still does not have ID.
I also downloaded the dbSNP vcf file from the NCBI database. I could not run the SnpSift Annotate of the ‘‘father vcf’’ against the NCBI dbSNP vcf, I guess it is because the chromosomes in the NCBI dbSNP vcf file are not named as ‘‘chr#’’ but only ‘’#’’.
Do I understand the error correctly? Any suggestions how I can solve this?