Hi all!
New here, introduction: I investigate inbreeding in an endangered species where I have whole genome data of several individuals and variants stored in VCF files.
I want to keep the file zipped (.vcf.gz) because of used memory etc.
Let's say I want to filter and keep only the SNPs with '--remove-indels' and using gzvcf, how do I make sure the output is not .vcf but also still compressed .vcf.gz ? And in the mean time nothing is unzipped? Because I get the idea VCFtools unzips everything in the mean time.. If I would use a pipeline and say gzip -c > output_file.vcf.gz this will not work right, because that compresses the output again but I do not want it to be uncompressed in the first place.
Help?!
Thanks
New here, introduction: I investigate inbreeding in an endangered species where I have whole genome data of several individuals and variants stored in VCF files.
I want to keep the file zipped (.vcf.gz) because of used memory etc.
Let's say I want to filter and keep only the SNPs with '--remove-indels' and using gzvcf, how do I make sure the output is not .vcf but also still compressed .vcf.gz ? And in the mean time nothing is unzipped? Because I get the idea VCFtools unzips everything in the mean time.. If I would use a pipeline and say gzip -c > output_file.vcf.gz this will not work right, because that compresses the output again but I do not want it to be uncompressed in the first place.
Help?!
Thanks
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