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.

  • $\begingroup$ You might consider vcfanno. $\endgroup$
    – user172818
    Nov 19, 2018 at 14:57

1 Answer 1


It would be useful if you show us some line of your CADD.bed and Input.vcf and how your desired output should look like.

bedtools is complaining about non positional records in CADD.bed, which means there are lines in this file where the first three columns aren't CHROM, START, END.

I guess you will have some header lines in the beginning that aren't introduced by an #. Just delete them (or add in # to the beginning of the line) and try again.

fin swimmer


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