Answers.Body: <p>It would be useful if you show us some line of your <code>CADD.bed</code> and <code>Input.vcf</code> and how your desired output should look like.</p>
  
  <p><code>bedtools</code> is complaining about non positional records in <code>CADD.bed</code>, which means there are lines in this file where the first three columns aren't <code>CHROM</code>, <code>START</code>, <code>END</code>.</p>
  
  <p>I guess you will have some header lines in the beginning that aren't introduced by an <code>#</code>. Just delete them (or add in <code>#</code> to the beginning of the line) and try again.</p>
  
  <p>fin swimmer</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-25T18:52:24.373Z
Answers.LastActivityDate: 2019-02-15T10:16:36.767Z
Answers.LastEditDate: 2019-02-15T10:16:36.767Z
Answers.UserDisplayName: finswimmer
Body: <p>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.</p>
  
  <p>This is the command I am using.</p>
  
  <pre><code>bedtools intersect -a CADD.bed -b Input.vcf| cut -f 3
  </code></pre>
  
  <p>But this command is giving me error</p>
  
  <pre><code>ERROR: file CADD.bed has non positional records, which are only valid for the groupBy tool.
  </code></pre>
  
  <p>Is there any way to solve this error or any other way to get RSID column in CADD output file.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-19T14:57:47.650Z
Comments.Text: You might consider [vcfanno](https://github.com/brentp/vcfanno).
Comments.UserDisplayName: user172818
Tags: <vcf><bedtools><variation>
Title: How to paste RSIDs in CADD output
ThreadText: # How to paste RSIDs in CADD output
  
  (Asked by: username_0 on 2018-11-14)
  
  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.
  
  **Tags:** vcf, bedtools, variation
  
  > **Comments:**
  > **username_1**: You might consider [vcfanno](https://github.com/brentp/vcfanno).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-11-25. Score: 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
  
  
  ---
  
  