I have around 9000+ vcf files that I'm trying to merge using bcftools merge. They are all located in their own folder so essentially I have a folder containing 9000+ separate folders, each containing one vcf.gz file.
I have tried out the following code via this tutorial
bcftools merge ~/path/to/folders/*.vcf.gz -Oz -o Merged.vcf.gz
However bcftools does not seem to recognize my command since I simply get this error:
About: Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file. Note that only records from different files can be merged, never from the same file. For "vertical" merge take a look at "bcftools norm" instead. Usage: bcftools merge [options] <A.vcf.gz> <B.vcf.gz> [...] Options: --force-samples resolve duplicate sample names --print-header print only the merged header and exit --use-header <file> use the provided header -0 --missing-to-ref assume genotypes at missing sites are 0/0 -f, --apply-filters <list> require at least one of the listed FILTER strings (e.g. "PASS,.") -F, --filter-logic <x|+> remove filters if some input is PASS ("x"), or apply all filters ("+") [+] -g, --gvcf <-|ref.fa> merge gVCF blocks, INFO/END tag is expected. Implies -i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max -i, --info-rules <tag:method,..> rules for merging INFO fields (method is one of sum,avg,min,max,join) or "-" to turn off the default [DP:sum,DP4:sum] -l, --file-list <file> read file names from the file -m, --merge <string> allow multiallelic records for <snps|indels|both|all|none|id>, see man page for details [both] --no-version do not append version and command line to the header -o, --output <file> write output to a file [standard output] -O, --output-type <b|u|z|v> 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v] -r, --regions <region> restrict to comma-separated list of regions -R, --regions-file <file> restrict to regions listed in a file --threads <int> number of extra output compression threads 
Any idea on what I'm doing wrong? Thanks!