Empty VCF files produced by both Mutect2 and HaplotypeCaller?

Question

[gprashant17]

I have tried using both Mutect2 and HaplotypeCaller (GATK) for calling somatic variants and generating VCF file from an aligned BAM file (RNA-seq). However, the generated VCF file did not have any information other than the header. I have seen this type of thread online, but I did not manage to find a solution. Is this because Base Recalibration was not done on the BAM file?

Meanwhile, when I try to use samtools mpileup on the same BAM file, the process aborts after a long time and it generates a VCF file of around 45GB.

[Asaf]

Can you samtools view -h you bam file?

[gprashant17]

Yes, I am able to view the bam files using samtools. I should mention here that I have used AddOrReplaceReadGroups (GATK) to include the @RG tag in the header, as it was not present initially.

[Ram]

It would help if you could show us all the output (STDOUT and STDERR) from the HaplotypeCaller run.

[gprashant17]

I'm not sure which output should I post. The command ran with no errors. It showed ProgressMeter for all the traversals and ended like this:

17:39:21.868 INFO  ProgressMeter - Traversal complete. Processed 10840980 total regions in 19.1 minutes.
17:39:21.915 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
17:39:21.915 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
17:39:21.916 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
17:39:21.916 INFO  Mutect2 - Shutting down engine
[21 June, 2019 5:39:21 PM IST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 19.87 minutes.
Runtime.totalMemory()=3141009408
Tool returned:
SUCCESS

[Ram]

Please give us the exact command and upload the entire log file to a GitHub Gist so we can work together and figure out what's happening.

Guide to GitHub Gist: A: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists

Also, if you're pasting text here, please use the formatting bar (especially the code option) to present it better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[igor]

This might the same problem/solution: Mutect2 (GATK4, Java8) outputs empty VCF file for tumor only mode