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Can GATK read compressed vcf files?

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
sequence snp genome
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updated by GouthamAtla GouthamAtla • written by Apprentice Apprentice

What error did you get ?

• 1 views • link
written by GouthamAtla GouthamAtla

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 
------------------------------------------------------------------------------------------
• 1 views • link
updated by Devon Ryan Devon Ryan • written by Apprentice Apprentice

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

?

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

The output was

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

• 1 views • link
written by Apprentice Apprentice

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
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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