VCF isnot compressed and indexed even after running bgzip and tabix,
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 !
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what are the outputs of
and
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
Hi Pierre,
Could you please let me know what is wrong with my vcf files.
Thank you !
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.vcfandtabix -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,