<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>

CC BY-SA 4.0
2018-11-25T18:52:24.373Z
2019-02-15T10:16:36.767Z
2019-02-15T10:16:36.767Z
finswimmer
<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>

CC BY-SA 4.0
2018-11-19T14:57:47.650Z
You might consider [vcfanno](https://github.com/brentp/vcfanno).
user172818
<vcf><bedtools><variation>
How to paste RSIDs in CADD output
# 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).  

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## 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


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