VCF isnot compressed and indexed even after running bgzip and tabix,

Question

[kirannbishwa01]

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 !

[Pierre Lindenbaum]

what are the outputs of

file mergedSNPsMY-min2.vcf.gz

and

file mergedSNPsMY-min2.vcf
head  mergedSNPsMY-min2.vcf

[kirannbishwa01]

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

[kirannbishwa01]

Hi Pierre,

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

Thank you !

[Jorge Amigo]

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,