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Identifying variants differing between control/treatment

I have a single multisample (48 samples) sample VCF file generated by GATK joint genotyping. I have further filtered by site level quality and such. Of these 48 samples, 24 samples are control and 24 samples are treatment. I am not so much interested between my samples vs reference. I am interested in variants that differ between my control and treated samples. How do I go about doing this? What is the workflow? What tools should I use?

gatk variant-calling snp indel
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by firestar firestar

1 answer

using vcfilterjdk http://lindenb.github.io/jvarkit/VcfFilterJdk.html

the following code declare two samples 'cases' S1 and S2, and two samples 'controls' S3 and S5. it then check that all cases have a different genotype than the controls.

 java -jar dist/vcffilterjdk.jar -e 'String cases[]=new String[]{"S1","S2"};String controls[]=new String[]{"S3","S4"}; for(final String S1:cases) {final Genotype G1=variant.getGenotype(S1); if(G1==null ||!G1.isCalled()) continue;for(final String S2:controls) {final Genotype G2=variant.getGenotype(S2); if(G2==null ||!G2.isCalled()) continue;   if(G1.sameGenotype(G2)) return false;}} return true;' input.vcf
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written by Pierre Lindenbaum Pierre Lindenbaum

So, in my case, I just need to replace S1, S2 etc with my sample aliases? Can I source them as a list of sample aliases in a text file?

control.txt

c1
c2
c3

treat.txt

t1
t2
t3
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written by firestar firestar 
sure:

$ java -jar dist/vcffilterjdk.jar --body -e 'List<String> cases = null,controls=null;  public Object apply(final VariantContext variant) { if(cases==null) try {cases=IOUtil.slurpLines(new java.io.File("treat.txt")) ; controls= IOUtil.slurpLines(new java.io.File("control.txt")); } catch(Exception e) {throw new RuntimeIOException(e);}; for(final String S1:cases) {final Genotype G1=variant.getGenotype(S1); if(G1==null ||!G1.isCalled()) continue;for(final String S2:controls) {final Genotype G2=variant.getGenotype(S2); if(G2==null ||!G2.isCalled()) continue;   if(G1.sameGenotype(G2)) return false;}} return true;}' input.vcf
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written by Pierre Lindenbaum Pierre Lindenbaum

Downloaded, compiled and ran this: java -jar vcffilterjdk.jar --help

Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
        at java.lang.Class.getDeclaredMethods0(Native Method)
        at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
        at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
        at java.lang.Class.getMethod0(Class.java:3018)
        at java.lang.Class.getMethod(Class.java:1784)
        at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
        at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException: com.beust.jcommander.ParameterException
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

I have checked if I have JAVA in my path echo ${PATH} /sw/comp/java/x86_64/sun_jdk1.8.0_92/bin

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written by firestar firestar

Checked all dependencies.

[rf@m1 dist]$ java -version
java version "1.8.0_92"
Java(TM) SE Runtime Environment (build 1.8.0_92-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.92-b14, mixed mode)

[rf@m1 dist]$ xsltproc --version
Using libxml 20706, libxslt 10126 and libexslt 815
xsltproc was compiled against libxml 20706, libxslt 10126 and libexslt 815
libxslt 10126 was compiled against libxml 20706
libexslt 815 was compiled against libxml 20706

[rf@m1 dist]$ make --version
GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.

[rf@m1 dist]$ git --version
git version 1.7.1

[rf@m1 dist]$ wget --version
GNU Wget 1.12 built on linux-gnu.
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written by firestar firestar

this is really strange... did you move the jar file ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Deleted all and reinstalled again. It works this time.

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written by firestar firestar

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