Variant Sampling programm

Question

[berndmann]

Hello,

Currently I'm looking for tool to sample variants from 1KG based on LD and MAF criteria. I found https://github.com/mulinlab/vSampler but it seems that this program is not working at least I tried both versions and it just produces some java class error.

I also found a post on biostar looking for something similar. But the SNPsnap tool by the Broad Institute is already offline.

Maybe someone found a good alternative in the meantime. The other biostars-post is almost 9 years old and still unanswered but I have hope that things changed up until today!

Best,
Berndmann

EDIT I:

java class error:

 java -jar  VariantSampler-1.0.2.jar 
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread "main" java.lang.ExceptionInInitializerError
    at org.mulinlab.variantsampler.cmdline.JarCommadLine.processAllCommandLinePrograms(JarCommadLine.java:96)
    at org.mulinlab.variantsampler.cmdline.JarCommadLine.extractCommandLineProgram(JarCommadLine.java:53)
    at org.mulinlab.variantsampler.cmdline.JarCommadLine.instanceMain(JarCommadLine.java:40)
    at org.mulinlab.variantsampler.cmdline.JarCommadLine.main(JarCommadLine.java:36)
Caused by: java.lang.UnsupportedOperationException: No class provided, and an appropriate one cannot be found.
    at org.apache.logging.log4j.LogManager.callerClass(LogManager.java:555)
    at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:580)
    at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:567)
    at org.broadinstitute.barclay.argparser.ClassFinder.<clinit>(ClassFinder.java:29)
    ... 4 more

[Pierre Lindenbaum]

h versions and it just produces some java class error.

show us those errors please.

[berndmann]

Edited the OP.

[Pierre Lindenbaum]

sorry, it looks like a known bug https://github.com/mulinlab/vSampler/issues/5 and the author didn't reply....

[Pierre Lindenbaum]

and the explanation is here: https://stackoverflow.com/questions/77593041

[berndmann]

That clarifies the problem for the vSampler but I guess such a sampling program is still a good thing to have. But it looks like no one was able so far to solve this task in a reasonable way. I hoped I could use an existing solution but it looks like I have to see if I can write a tool in C with some help of the bcftools library.

Thanks for your time, anyway.

[berndmann]

I managed to get the program running in some docker container with JDK8. Sadly the obscure database they rely on is also not available anymore. But I found all the necessary files to recreate this. I will open a github repo where I add all the docker files and a link to a database once I'm sure that everything works as expected.