Combine two VCF files with GATK4

Question

[MAPK]

Hi All,

I have been trying to combine two VCF files with file1.vcf with samples A,B,C and file2.vcf with samples D,E,F. I tried tools like GatherVcfs, MergeVcfs, but they both fail. What is the right tool I should be using to do this? There was CombineVariants tool in GATK3, which is not available in GATK4.

TIA

Answer 1

[tothepoint]

You may need to use picard tool to merge files.

java -jar path_to_picard.jar MergeVcfs I=file1.csf I=file2.vcf O=merged.vcf.gz

or try bcftools merge option

bcftools merge --merge all file1.vcf.gz file2.vcf.gz -O v -o merged.vcf.gz

[MAPK]

@devarora they (MergeVcfs) both are same, either you use via GATK or Picard. I get the same error.

[tothepoint]

did you tried bcftools merge option also?

[MAPK]

bcftools works. Thank you.

[Vimala]

Yes it is working

[Ram]

Do not add an answer unless you're answering the top-level question. If you wish to provide feedback on an answer, use Add Comment or Add Reply instead as appropriate. I'll move this "answer" to a comment on the most upvoted answer, feel free to move it elsewhere if you were commenting on a different answer.

Answer 2

[DareDevil]

MergeVcfs from gatk should work (gatk v4.1.1)

gatk --java-options '-Xmx60g' \
MergeVcfs -I file1.vcf -I file2.vcf -I file3.vcf \
-O combined.vcf

What do you mean by 'they fail' ? What is the error you are getting there?

[MAPK]

@dare_devil

The samples in file1.vcf.gz and file2.vcf.gz are different (like I said, this is what I want to combine), so this is the error I am getting:

[Sun Jan 17 22:03:33 CST 2021] MergeVcfs  --INPUT File1.vcf.gz --INPUT File2.vcf.gz --OUTPUT OUTfile.vcf.gz  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX true --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Jan 17, 2021 10:03:35 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Sun Jan 17 22:03:35 CST 2021] Executing as [e-mail] on Linux 3.10.0-1127.13.1.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_171-b11; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.2.0
[Sun Jan 17 22:03:35 CST 2021] picard.vcf.MergeVcfs done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=4362600448
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.lang.IllegalArgumentException: Input file /Seq_Data/File1.vcf.gz has sample entries that don't match the other files.
        at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:203)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
        at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
        at org.broadinstitute.hellbender.Main.main(Main.java:291)

[DareDevil]

you can try a python package bioinfokit to deal with this

from bioinfokit.analys import marker
# concatenate VCF files. You can provide multiple VCF files separated by comma.
 marker.concatvcf("file_1.vcf,file_2.vcf,file_3.vcf,file_4.vcf")
# merged VCF files will be stored in same directory (concat_vcf.vcf)

[svp]

MergeVcfs of gatk will not work with different entries

Answer 3

[svp]

Try using snpsift

java -jar SnpSift.jar split -j *.vcf > combined.vcf