SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Updated How to convert .txt file to .bed .GFF or .BAR file format, forevermark4 Bioinformatics 2 06-30-2014 06:02 AM
How to convert .txt file to .bed or .gff, How can we use chip seq data in R software forevermark4 Bioinformatics 57 06-30-2014 06:01 AM
Is there a BED file format validator? Does a BED file have to be sorted position? LauraSmith Bioinformatics 3 05-21-2013 12:54 PM
how to convert SAM file to BED or MUT marufdu07 General 2 02-07-2012 03:20 AM
How to convert eland file to BED format huo Bioinformatics 1 01-19-2011 11:43 AM

Reply
 
Thread Tools
Old 02-06-2010, 12:24 PM   #1
Ling
Junior Member
 
Location: Berkeley, CA

Join Date: Jan 2010
Posts: 8
Default Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools?

Hi all,

To locate the SNPs in a SNP.txt file to each of coding gene exons I need to convert the TXT to a bed file in order to use BEDTools. Is there any way to do is? or is there any way to get a SNP.bed output from samtools?

Any inputs are highly appreciated, thank!


Ling
Ling is offline   Reply With Quote
Old 02-06-2010, 03:38 PM   #2
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

Read this thread, you'll find the solution there:

http://seqanswers.com/forums/showthread.php?t=2446
__________________
-drd
drio is offline   Reply With Quote
Old 02-06-2010, 06:39 PM   #3
Ling
Junior Member
 
Location: Berkeley, CA

Join Date: Jan 2010
Posts: 8
Default

Hi Drio,

Thank you for your message.

But it seemed to me those were only for converting a sam/bam to a bed file. I am seeking ways to convert the output (.txt) from samtools pileup to a bed file, which may not make sense, sorry.

Best,

Ling
Ling is offline   Reply With Quote
Old 02-06-2010, 07:33 PM   #4
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

Quote:
Originally Posted by Ling View Post
Hi Drio,

Thank you for your message.

But it seemed to me those were only for converting a sam/bam to a bed file. I am seeking ways to convert the output (.txt) from samtools pileup to a bed file, which may not make sense, sorry.

Best,

Ling
Right, sorry. Why don't you write a quick script yourself?
__________________
-drd
drio is offline   Reply With Quote
Old 06-30-2014, 06:02 AM   #5
inesdesantiago
Member
 
Location: LONDON, UNITED KINGDOM

Join Date: Jan 2009
Posts: 44
Default

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
inesdesantiago is offline   Reply With Quote
Old 04-01-2015, 07:46 AM   #6
vd4mindia
Member
 
Location: Milan

Join Date: May 2013
Posts: 40
Default

@inesdesantiago
I have a situation where I have output of SNPs from VarScan. I see the varscan outputs LOH( both as SNP and INDELS LOH). Now for INDELS its fairly easy to make a bed format file. But for SNP -LOH if I want to make the bed file what should be the trick. I know that for a SNP the base which is changed can be either start of chromosome and the next base can be the stop site or the base that is a variant can be the stop coordinate and its previous base can be the start. however if you you have situation like below. How should this be performed? Can your tool make bed files from SNP-LOH regions from this kind of situation or always it is needed to supply the genomic intervals?

Quote:
chr Position Depth
1 1654067 65
1 1654068 63
I would like to know how can this situation be handled?
vd4mindia is offline   Reply With Quote
Old 04-02-2015, 06:58 AM   #7
diego diaz
Member
 
Location: Santiago, Chile

Join Date: Oct 2013
Posts: 62
Default

Sorry my ignorance but, can awk be useful for that?

Please post some lines of your input file and some lines of your expected output file. I may help you with a awk sentence.
diego diaz is offline   Reply With Quote
Old 04-02-2015, 07:17 AM   #8
vd4mindia
Member
 
Location: Milan

Join Date: May 2013
Posts: 40
Default

No I have already figured out a tool that works best for this.. the bedops tool has a function vcf2bed works fit to convert the scenario and I already performed that and also am familiar with awk as well. Infact I was more concerned if the conversion is 1 based or 0 based. But that issue is solved for me. Thanks a lot.
vd4mindia is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:25 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO