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Convert BED(UCSC) to VCF

I am using liftOver to convert hg19-hg38. I made BED file from VCF to run liftOver. How can I convert output BED(HG38) to VCF format.

assembly
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updated by guntul • guntul • written by Ishtiaq Ahmad Khan Ishtiaq Ahmad Khan

1 answer

Instead of doing multiple conversions, you can use CrossMap to convert VCF (hg19) <-> VCF (hg38). Other than VCF, it can support SAM/BAM, Wiggle/BigWig, BED, GFF/GTF file formats.

Or you can use NCBI remap.

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updated by Ram Ram • written by komal.rathi komal.rathi

Thank you komal. I have installed CrossMap. I tried to run

python CrossMap.py

It generates following error message

Traceback (most recent call last):
  File "CrossMap.py", line 26, in <module>
    from cmmodule  import ireader
ImportError: No module named cmmodule

Do you think it is not properly installed?

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updated by Ram Ram • written by Ishtiaq Ahmad Khan Ishtiaq Ahmad Khan

What python version did you use?

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written by Zaag Zaag

cmmodule is a directory within CrossMap lib that contains python modules for CrossMap.py. I can think of two ways you can add the lib directory to your python path. You can do it in BASH by running something like

export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHONPATH

taken from here: http://crossmap.sourceforge.net/#installation

After you export the directory to PYTHONPATH, you should be able to run CrossMap as usual. I don't like doing this since then it's in my path until my next logout. More importantly, I'll have to remember to export PYTHONPATH in every new session where I want to run CrossMap, and I know I'll forget this.

Instead, I added these three lines to my code just before import optparse, and the script adds lib to the python path on its own:

PARENTPATH = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
LIBPATH = os.path.join(PARENTPATH, "lib")
sys.path.append(LIBPATH)

As long as bin and lib are sister directories, this should work. Let me know if you want any more explanation about why it does.

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updated by Ram Ram • written by Mitch Bekritsky Mitch Bekritsky

Sir, I am having the same problem about running Crossmap. I got the same cmmodule error. But since I have python through home-brew. I guess it caused a problem. Could you help to solve my problem ? or I you could teach me how to catch a fish I would also be glad. Thank you very much for your help.

edit:

btw, my python site packages are located the path below.

/usr/local/lib/python2.7/site-packages
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updated by Ram Ram • written by morovatunc morovatunc

I successfully run CrossMap. It was my first experience at Biostars and happened to be so nice. Thank you very much for your help.

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updated by Ram Ram • written by Ishtiaq Ahmad Khan Ishtiaq Ahmad Khan

Just curious--did you end up using either of my tweaks? Which one ended up working for you?

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updated by Ram Ram • written by Mitch Bekritsky Mitch Bekritsky

I tried first and it worked.

export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHONPATH
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updated by Ram Ram • written by Ishtiaq Ahmad Khan Ishtiaq Ahmad Khan

I am trying CrossMap but it requires chain file. Is there any way without using chain file?

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written by guntul • guntul

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