How to merge vcf files (output of VarScan2 somatic)?

Question

[Raheleh]

Hello,

I have WES data of tumor samples with matched ones extracted from 13 patients (paired-end, illumina). I used BWA mem to align them against hg38, and used VarScan2 to call somatic variations. Now I have 6 files (fpfilter_Passed.vcf) for each patient (Somatic, LOH, Germline for each of snp and indel variations).

I am trying to merge the vcf files of each patient using CombineVariants and MergeVcfs (Picard) of gatk, but no success yet. Can any one tell me if I am on the right way? Is there any other tools that I can try?

Thanks for any help!

Answer 1

[finswimmer]

bcftools merge should be the answer ;)

For this you have to gzip and index each vcf file first

$ bgzip -c sample1.vcf > sample1.vcf.gz
$ tabix sample1.vcf.gz

Then you can use:

$ bcftools merge sample1.vcf.gz sample2.vcf.gz ... > merged.vcf

I am trying to merge the vcf files of each patient using CombineVariants and MergeVcfs (Picard) of gatk, but no success yet.

What was the problem?

fin swimmer

[Raheleh]

many thanks for your reply. This is my command:

java -jar GenomeAnalysisTK.jar -T CombineVariants -R hg38.fa --variant Germline.hc.fpfilterPassed.vcf --variant Somatic.hc.fpfilterPassed.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY

And this is the error when I am using CombineVariants:

Error: Unable to access jar file GenomeAnalysisTK.jar

there is no any jar file with the mentioned name in the downloaded package (gatk-4.0.11.0). after many search I found that may be replacing java -jar GenomeAnalysisTK.jar by gatk can solve the problem. But I got this error:

A USER ERROR has occurred: '-T' is not a valid command.

I tried without -T, but no success.

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Regarding MergeVCFs tools: This is the command: (I got this command from the recommended workflow of the website)

java -jar picard.jar MergeVcfs I=Germline.hc.fpfilterPassed.vcf  I=Somatic.hc.fpfilterPassed.vcf O=Output.vcf.gz

When I run the command I got this:

NOTE: Picard's command line syntax is changing.

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** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

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** The command line looks like this in the new syntax:

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** MergeVcfs -I Germline.hc.fpfilterPassed.vcf -I Somatic.hc.fpfilterPassed.vcf -O Output.vcf.gz

I tried this command:

  java -jar picard.jar MergeVcfs -I Germline.hc.fpfilterPassed.vcf  -I Somatic.hc.fpfilterPassed.vcf -O Output.vcf.gz

But I got this error:

ERROR: Invalid argument '-I'

Please help me to get out of this problem. Many thanks!

[finswimmer]

Hello,

gatk's CombineVariants isn't available in gatk4. And I think this tool doesn't do what you like to do. It's for combining variants from the same sample into a single file. But you like to have different samples in one file.

The message by MergeVcfs is just a notice. It should produce a valid output.

fin swimmer

[Raheleh]

Thank you fin swimmer. Yes it produced an output but just headers are there no more.

Edit: Sorry I made a mistake. It produces nothing. I mean after getting that notice, I get no outputs.