diff --git a/src/bcftools/bcftools_concat/help.txt b/src/bcftools/bcftools_concat/help.txt new file mode 100644 index 00000000..fc0f1914 --- /dev/null +++ b/src/bcftools/bcftools_concat/help.txt @@ -0,0 +1,36 @@ +``` +bcftools concat -h +``` + +concat: option requires an argument -- 'h' + +About: Concatenate or combine VCF/BCF files. All source files must have the same sample + columns appearing in the same order. The program can be used, for example, to + concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel + VCF into one. The input files must be sorted by chr and position. The files + must be given in the correct order to produce sorted VCF on output unless + the -a, --allow-overlaps option is specified. With the --naive option, the files + are concatenated without being recompressed, which is very fast. +Usage: bcftools concat [options] [ [...]] + +Options: + -a, --allow-overlaps First coordinate of the next file can precede last record of the current file. + -c, --compact-PS Do not output PS tag at each site, only at the start of a new phase set block. + -d, --rm-dups STRING Output duplicate records present in multiple files only once: + -D, --remove-duplicates Alias for -d exact + -f, --file-list FILE Read the list of files from a file. + -l, --ligate Ligate phased VCFs by matching phase at overlapping haplotypes + --ligate-force Ligate even non-overlapping chunks, keep all sites + --ligate-warn Drop sites in imperfect overlaps + --no-version Do not append version and command line to the header + -n, --naive Concatenate files without recompression, a header check compatibility is performed + --naive-force Same as --naive, but header compatibility is not checked. Dangerous, use with caution. + -o, --output FILE Write output to a file [standard output] + -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v] + -q, --min-PQ INT Break phase set if phasing quality is lower than [30] + -r, --regions REGION Restrict to comma-separated list of regions + -R, --regions-file FILE Restrict to regions listed in a file + --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1] + --threads INT Use multithreading with worker threads [0] + -v, --verbose 0|1 Set verbosity level [1] +