Is it possible to convert a SNP.txt to a bed file or get a SNP.bed from samtools?

Ling · 02-06-2010, 11:24 AM

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

drio · 02-06-2010, 02:38 PM

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

http://seqanswers.com/forums/showthread.php?t=2446

Ling · 02-06-2010, 05:39 PM

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

drio · 02-06-2010, 06:33 PM

Quote:

Originally Posted by Ling

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?

inesdesantiago · 06-30-2014, 05:02 AM

You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html

vd4mindia · 04-01-2015, 06:46 AM

@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?

diego diaz · 04-02-2015, 05:58 AM

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.

vd4mindia · 04-02-2015, 06:17 AM

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.

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02-06-2010, 11:24 AM	#1
Ling Junior Member Location: Berkeley, CA Join Date: Jan 2010 Posts: 8	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

02-06-2010, 02:38 PM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	Read this thread, you'll find the solution there: http://seqanswers.com/forums/showthread.php?t=2446 __________________ -drd

02-06-2010, 05:39 PM	#3
Ling Junior Member Location: Berkeley, CA Join Date: Jan 2010 Posts: 8	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

06-30-2014, 05:02 AM	#5
inesdesantiago Member Location: LONDON, UNITED KINGDOM Join Date: Jan 2009 Posts: 44	You could also use GenomeIntervals2BED.py script available within the SeqGI framework. Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html

04-02-2015, 05:58 AM	#7
diego diaz Member Location: Santiago, Chile Join Date: Oct 2013 Posts: 62	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.

04-02-2015, 06:17 AM	#8
vd4mindia Member Location: Milan Join Date: May 2013 Posts: 40	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.