Hi I would like to make statistics from vcf.gz files using bcftools stats, but when I try to run the following script, it generates files without weight my script is this:
> bcftools stats -F "My_reference_genome.fasta" -s "My_vcf.gz_file.vcf.gz" > "/T1_.vcf.stats"
Immediately ran the script it get me the following on the command screen:
About: Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. When two files are given, the program generates separate stats for intersection and the complements. By default only sites are compared, -s/-S must given to include also sample columns. Usage: bcftools stats [options] <A.vcf.gz> [<B.vcf.gz>] Options: --af-bins <list> allele frequency bins, a list (0.1,0.5,1) or a file (0.1\n0.5\n1) --af-tag <string> allele frequency tag to use, by default estimated from AN,AC or GT -1, --1st-allele-only include only 1st allele at multiallelic sites -c, --collapse <string> treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none] -d, --depth <int,int,int> depth distribution: min,max,bin size [0,500,1] -e, --exclude <expr> exclude sites for which the expression is true (see man page for details) -E, --exons <file.gz> tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed) -f, --apply-filters <list> require at least one of the listed FILTER strings (e.g. "PASS,.") -F, --fasta-ref <file> faidx indexed reference sequence file to determine INDEL context -i, --include <expr> select sites for which the expression is true (see man page for details) -I, --split-by-ID collect stats for sites with ID separately (known vs novel) -r, --regions <region> restrict to comma-separated list of regions -R, --regions-file <file> restrict to regions listed in a file -s, --samples <list> list of samples for sample stats, "-" to include all samples -S, --samples-file <file> file of samples to include -t, --targets <region> similar to -r but streams rather than index-jumps -T, --targets-file <file> similar to -R but streams rather than index-jumps -u, --user-tstv <TAG[:min:max:n]> collect Ts/Tv stats for any tag using the given binning [0:1:100] --threads <int> number of extra decompression threads  -v, --verbose produce verbose per-site and per-sample output
If anyone could help me, I'd be very grateful. thanks