Question: How to convert VCF to BED without BEDOPS
gravatar for charles.kronk
3.6 years ago by
charles.kronk10 wrote:

So I'm trying to find the closest features to a set of SNPs using something along the lines of:

closest-features --closest --dist <(vcf2bed snps.vcf) hg38.bed > answer.bed

But unfortunately, since I am on a Windows machine running Cygwin, there was an error in the makefile and I get the error:

Error: Cannot find sort-bed binary required for sorting BED output

Digging further, I found that this did not install correctly because after running make, I get this:

SortDetails.cpp: In function 'FILE* createTmpFile(const char*, char**)':
SortDetails.cpp:132:22: error: 'mkstemp' was not declared in this scope
     fd = mkstemp(tmpl);
SortDetails.cpp:138:26: error: 'fdopen' was not declared in this scope
     fp = fdopen(fd, "wb+");

As far as I can tell, this messes with the install of sort-bed because when I run make install I get this:

cp applications/bed/sort-bed/bin/sort-bed- bin/sort-bed
make: [Makefile:75: install] Error 1 (ignored)
cp: cannot stat 'applications/bed/sort-bed/bin/update-sort-bed-slurm-': No such file or directory

There is, as it says, no "sort-bed" in the bin folder of bedops.

I haven't been able to find anything substantial in solving this problem so my questions are:

  1. Is there some online portal like Galaxy that can convert vcf to bed? The only step of this which seems to effect me is the conversion step, so if I can get a bed file from my snps.vcf I should be able to proceed.
  2. Has anyone run into this sort of thing before? Is it impossible to get bedops on Cygwin fully? Any sort of work-around?
  3. Should I just bypass this whole thing? My goal is to use these SNPs to link them to closest features and then run those features through some sort of pathway analysis software to look for patterns or associations that might be related to my given phenotype... Is this the totally wrong way to go about it?

Thank you so much, this is my first post here and if any of this is against the rules or needs to be changed, please let me know and I'll edit and/or remove it!

snp vcf software error • 1.3k views
ADD COMMENTlink written 3.6 years ago by charles.kronk10

since I am on a Windows machine running Cygwin

Do you still need Cygwin when Windows 10 can run many linux applications natively?

ADD REPLYlink written 3.6 years ago by WouterDeCoster45k

At least with my machine, yes. There is no Windows-based build for BEDOPS, so I am limited to Cygwin (which I have found some support for this decision online, but if you happen to know a way around it, please let me know).

ADD REPLYlink written 3.6 years ago by charles.kronk10

If you can post what versions of Cygwin, gcc and glibc you have installed, I can look at trying to fix this. No guarantees, but let me know if you're interested in investigating this more.

ADD REPLYlink written 3.6 years ago by Alex Reynolds31k

It has been forever since I posted this and I've forgot to check back honestly... I've utilized a workaround to manually convert the files (I downloaded some BED files from UCSC and then used a python script to convert the VCF to look like them).

But just in case this helps anyone else, I'm willing to put out these specs for future diagnostics!

"uname -a" returns "CYGWIN_NT-10.0 DESKTOP-U41RDVC 2.8.2(0.313/5/3) 2017-07-12 10:58 x86_64 Cygwin" "uname -r" thus returns "2.8.2(0.313/5/3)"

(So I'm pretty sure the Cygwin version is 2.8.2(0.313/5/3).

The gcc version is "5.4.0 (GCC)" (per running "gcc -v").

The glibc version I have seen online that I can find by running "ldd --version" which returns "ldd (cygwin) 2.8.2".

Please let me know if you need anything else! Absolutely no rush on this, but it might help someone else struggling!

ADD REPLYlink written 3.6 years ago by charles.kronk10
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