I want to paste RSIDs in CADD output as CADD does not give RSID column in its output. For this purpose I am using bedtools intersect to compare two files and have RSID column in my CADD file.
This is the command I am using.
bedtools intersect -a CADD.bed -b Input.vcf| cut -f 3
But this command is giving me error
ERROR: file CADD.bed has non positional records, which are only valid for the groupBy tool.
Is there any way to solve this error or any other way to get RSID column in CADD output file.