Can GATK read compressed vcf files?

Question

[Apprentice]

Hi!

I have one question about GATK CombineVariants.

Could you tell me whether　GATK CombineVariants can load compressed vcf files?

Below command returned error.

java -jar GenomeAnalysisTK.jar   -T CombineVariants   -R reference.fasta   --variant input1.vcf.gz  --variant input2.vcf.gz   -o output.vcf

[GouthamAtla]

What error did you get ?

[Apprentice]

The message is shown as below;

------------------------------------------------------------------------------------------
Done. There were 2 WARN messages, the first 2 are repeated below.
WARN  18:47:51,038 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, sjavascript:document.forms["comment-form"].submit()kipping dictionary validation 
WARN  18:47:51,039 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation 
------------------------------------------------------------------------------------------

[Pierre Lindenbaum]

I'm afraid it's not a vcf file. It looks like a file downloaded from the web. Anyway, vcf.gz files must be compressed with bgzip and indexed with tabix.

what's the output of :

file input1.vcf.gz   input2.vcf.gz

?

[Apprentice]

The output was

input1.vcf.gz: gzip compressed data, extra field input2.vcf.gz: gzip compressed data, extra field

[Pierre Lindenbaum]

ok, so it's correct. It's clearly a set of bzipped files.

Can you now show me the output of:

gunzip -c input1.vcf.gz | grep -v "#" | head -n 2