Question: VCF isnot compressed and indexed even after running bgzip and tabix,
gravatar for kirannbishwa01
4.3 years ago by
United States
kirannbishwa011.2k wrote:

After compressing and indexing my vcf file for parsing using the following commands:

gunzip mergedSNPsMY-min2.vcf.gz

bgzip mergedSNPsMY-min2.vcf

tabix -p vcf mergedSNPsMY-min2.vcf.gz

I am still getting the error message: DEBUG: 2016-04-26 17:34:35,611: File is not compressed

What could be going wrong?

Thank you in advance !

compression tabix bgzip vcf • 1.5k views
ADD COMMENTlink written 4.3 years ago by kirannbishwa011.2k

what are the outputs of

file mergedSNPsMY-min2.vcf.gz


file mergedSNPsMY-min2.vcf
head  mergedSNPsMY-min2.vcf
ADD REPLYlink written 4.3 years ago by Pierre Lindenbaum129k

file passed_SNPsMA622.vcf.gz

passed_SNPsMA622.vcf.gz: gzip compressed data, extra field

file passed_SNPsMA622.vcf

passed_SNPsMA622.vcf: ASCII text, with very long lines

head passed_SNPsMA622.vcf This prints some parts of the vcf file on the terminal, basically. - not shown here

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by kirannbishwa011.2k

Hi Pierre,

Could you please let me know what is wrong with my vcf files.

Thank you !

ADD REPLYlink written 4.3 years ago by kirannbishwa011.2k

your code should work unless mergedSNPsMY-min2.vcf.gz is not well formed, and the way to check this is to follow Pierre's instructions. but have you tried using the -f (force) option with bgzip -f file.vcf and tabix -fp vcf file.vcf.gz? if you had existing files your code should have complained, asking to overwrite previous files, but I'm just willing to provide some more options,

ADD REPLYlink written 4.3 years ago by Jorge Amigo11k
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