Question: Can GATK read compressed vcf files?
0
gravatar for Apprentice
4.1 years ago by
Apprentice40
Apprentice40 wrote:

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
snp sequence genome • 3.8k views
ADD COMMENTlink modified 4.1 years ago by geek_y11k • written 4.1 years ago by Apprentice40

What error did you get ?

ADD REPLYlink written 4.1 years ago by geek_y11k

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 
------------------------------------------------------------------------------------------
ADD REPLYlink modified 4.1 years ago by Devon Ryan97k • written 4.1 years ago by Apprentice40
1

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

?

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k

The output was

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

ADD REPLYlink written 4.1 years ago by Apprentice40

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
ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k
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