Convert BCF to BAM

Question

[taniamahmood38]

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

[Pierre Lindenbaum]

converting a bcf to a bam is like creating a cow from a steak.

[taniamahmood38]

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

[Pierre Lindenbaum]

./gradlew --stacktrace vcf2bam

[taniamahmood38]

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

[Pierre Lindenbaum]

which OS ? which java version ?

[taniamahmood38]

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

[Pierre Lindenbaum]

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

[taniamahmood38]

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

[Pierre Lindenbaum]

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.

[taniamahmood38]

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

[Pierre Lindenbaum]

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

[rgsingleton]

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?

[Pierre Lindenbaum]

see https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference

Answer 1

[Pierre Lindenbaum]

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