# Extraction of bed files based on rsids

**URL:** <https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415>\
**Category:** Feature Requests\
**Created:** [January 29, 2018, 11:19pm UTC](https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415 "2018-01-29T23:19:48Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![akhilpampana](https://avatars.discourse-cdn.com/v4/letter/a/e480ec/32.png) [@akhilpampana](https://discuss.hail.is/u/akhilpampana)\
**Post date:** [January 29, 2018, 11:19pm UTC](https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415/1 "2018-01-29T23:19:48Z")

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Hello everyone,  
Congratulations and waiting for 0.2 to roll out.

I had been working on extraction of variant information and working on gwas data and i thought of extracting data by means of rsid. I think it will be helpful as each variant have rsids and can be very easy in mapping. and i think it also solves the transcripts problem(like one variant have many transcripts when rsid is used for extraction each have their own rsid which helps in extraction)

Thank you

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [January 31, 2018, 3:40pm UTC](https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415/2 "2018-01-31T15:40:03Z")

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Hi Akhil,  
can you give an example of the input and output you’d like to see? The variant annotations / bed file that should get produced.

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**Author:** ![akhilpampana](https://avatars.discourse-cdn.com/v4/letter/a/e480ec/32.png) [@akhilpampana](https://discuss.hail.is/u/akhilpampana)\
**Post date:** [January 31, 2018, 10:55pm UTC](https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415/3 "2018-01-31T22:55:58Z")

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Sorry tim for the late reply. basically its like this. if we have chrom regions along with rsids , we can extract the genes with corresponding snps informaiton based on rsids.( i dont know what i mentioned is correct or not)

Input:

| chrom | start | end | snps | P\_VALUE | disease |
| --- | --- | --- | --- | --- | --- |
| chr1 | 203155882 | 203155882 | rs4950928 | 1.00E-13 | YKL-40 levels |
| chr13 | 40350912 | 40350912 | rs7993214 | 2.00E-06 | Psoriasis |
| chr15 | 78806023 | 78806023 | rs8034191 | 3.00E-18 | Lung cancer |
| chr1 | 159680868 | 159680868 | rs2808630 | 7.00E-06 | Lung cancer |
| chr3 | 190350461 | 190350461 | rs7626795 | 8.00E-06 | Lung cancer |

output should be like this in bed file format:

`rsid chr TSS TTS genes_present_in_that_region` and if possible we can extract the variants based on rsids near Transcriptions start site using rsids?

I dont know whether its possible or not but just an idea

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [January 31, 2018, 10:58pm UTC](https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415/4 "2018-01-31T22:58:15Z")

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Ah, so you need to take the information in the table and find variants nearby? e.g. the chr1:203155882 line should find variants on chr1 nearby 203155882.

That’s something that totally _should_ be possible in Hail, but I’m not sure how to do it right now.

Let’s explore when 0.2 is out!

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**Author:** ![akhilpampana](https://avatars.discourse-cdn.com/v4/letter/a/e480ec/32.png) [@akhilpampana](https://discuss.hail.is/u/akhilpampana)\
**Post date:** [January 31, 2018, 11:14pm UTC](https://discuss.hail.is/t/extraction-of-bed-files-based-on-rsids/415/5 "2018-01-31T23:14:04Z")

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ya thats the exact information i need. so thought of asking why not keep that kind of functionality in hail.