Convert BCF to BAM
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21 months ago

Hiii, I want to know the command line to convert BCF to BAM file on terminal (Linux). Kindly help me out. Thanks in advance

BCF to BAM Linux Ubuntu terminal Command line • 832 views
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converting a bcf to a bam is like creating a cow from a steak.

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Thanks a lot for your help. Now i have VCF file and i have downloaded jvarkit-master. Now when i am downloading and compiling dependencies i am getting error when i run this command ./gradlew vcf2bam. The error is FAILURE: Build failed with an exception.

What went wrong: Could not create an instance of type org.gradle.initialization.DefaultSettings_Decorated.

    Could not initialize class org.codehaus.groovy.runtime.InvokerHelper

Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

Get more help at https://help.gradle.org

BUILD FAILED in 0s

Will you please help me to resolve it ? Thanks

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./gradlew --stacktrace vcf2bam
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I am getting the same error. I have tried all possible options ./gradlew --stacktrace vcf2bam ./gradlew --scan vcf2bam ./gradlew --debug vcf2bam ./gradlew --info vcf2bam

I am really sorry to trouble you again and again

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which OS ? which java version ?

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Ubuntu (Linux OS). Secondly i have put my jvarkit-master in java 11 folder and has given path to it.

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and there is no stacktrace ? only this message " Could not initialize class org.codehaus.groovy.runtime.InvokerHelper" ?

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when i run this command ./gradlew --stacktrace vcf2bam the error occurs is FAILURE: Build failed with an exception.

  • What went wrong: Could not create an instance of type org.gradle.initialization.DefaultSettings_Decorated.

    Could not initialize class org.codehaus.groovy.runtime.InvokerHelper

  • Try: Run with --info or --debug option to get more log output. Run with --scan to get full insights.

  • Exception is: org.gradle.api.reflect.ObjectInstantiationException: Could not create an instance of type org.gradle.initialization.DefaultSettings_Decorated. . . . . .

    Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.codehaus.groovy.runtime.InvokerHelper at org.gradle.api.internal.plugins.DefaultExtraPropertiesExtension.<init>(DefaultExtraPropertiesExtension.java:29) at org.gradle.api.internal.plugins.DefaultConvention.<init>(DefaultConvention.java:47) at org.gradle.api.internal.ExtensibleDynamicObject.<init>(ExtensibleDynamicObject.java:58) at org.gradle.initialization.DefaultSettings.<init>(DefaultSettings.java:93) at org.gradle.initialization.DefaultSettings_Decorated.<init>(Unknown Source) at jdk.internal.reflect.GeneratedConstructorAccessor10.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at org.gradle.internal.reflect.DirectInstantiator.newInstance(DirectInstantiator.java:51) ... 100 more

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I just updated the gradle ( build-automation system ) for this tool. https://github.com/lindenb/jvarkit/commit/0d69d16fb9d675ec630d313b937b67dd5a58024b . Can you try with this new version. If it still fails, I've no idea how to fix this.

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Sure i will try and thank you so much for your kind and quick responses @Pierre Lindenbaum.

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hum sorry, no idea how to fix this. Try to compile this on another computer ?

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I had a question about the reference file format for the vcf2bam tool. I know how to index a fasta file and how to make a sequence dictionary, but I keep getting errors for trying to do both. How do you generate the correct reference file?

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21 months ago

i wrote a vcf2bam. http://lindenb.github.io/jvarkit/VcfToBam.html

I hardly ever used it.

you have to first convert the bcf to vcf with bcftools view

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