The 8-bit format uses the C0 and C1 control characters and ASCII charactersfrom the Multinational character set. The sequences also show each character'scolumn/row position in the character set table, below the character. The column/row code eliminates confusion over similar-looking characters such as 0 (3/0) andO (4/15).
Csi Column V 8 1
The following terminal sequences are intercepted by the console host when written into the output stream, if the ENABLE_VIRTUAL_TERMINAL_PROCESSING flag is set on the screen buffer handle using the SetConsoleMode function. Note that the DISABLE_NEWLINE_AUTO_RETURN flag may also be useful in emulating the cursor positioning and scrolling behavior of other terminal emulators in relation to characters written to the final column in any row.
As these sequences were different for different terminals, elaborate libraries such as termcap ("terminal capabilities") and utilities such as tput had to be created so programs could use the same API to work with any terminal. In addition, many of these terminals required sending numbers (such as row and column) as the binary values of the characters; for some programming languages, and for systems that did not use ASCII internally, it was often difficult to turn a number into the correct character.
Regions can be specified either on command line or in a VCF, BED, ortab-delimited file (the default). The columns of the tab-delimited filecan contain either positions (two-column format) or intervals (three-columnformat): CHROM, POS, and, optionally, END, where positions are 1-basedand inclusive. The columns of the tab-delimited BED file are alsoCHROM, POS and END (trailing columns are ignored), but coordinatesare 0-based, half-open. To indicate that a file be treated as BED ratherthan the 1-based tab-delimited file, the file must have the ".bed" or".bed.gz" suffix (case-insensitive). Uncompressed files are stored inmemory, while bgzip-compressed and tabix-indexed region files are streamed.Note that sequence names must match exactly, "chr20" is not the same as"20". Also note that chromosome ordering in FILE will be respected,the VCF will be processed in the order in which chromosomes first appearin FILE. However, within chromosomes, the VCF will always beprocessed in ascending genomic coordinate order no matter what order theyappear in FILE. Note that overlapping regions in FILE can result induplicated out of order positions in the output.This option requires indexed VCF/BCF files. Note that -R cannot be usedin combination with -r.
File of sample names to include or exclude if prefixed with "^".One sample per line. See also the note above for the -s, --samplesoption.The sample order is updated to reflect that given in the input file.The command bcftools call accepts an optional secondcolumn indicating ploidy (0, 1 or 2) or sex (as defined by--ploidy, for example "F" or "M"), for example:
If the second column is not present, the sex "F" is assumed.With bcftools call -C trio, PED file is expected.The program ignores the first column and the last indicates sex (1=male, 2=female), for example:
With the call -C alleles command, third column of the targets file mustbe comma-separated list of alleles, starting with the reference allele.Note that the file must be compressed and indexed.Such a file can be easily created from a VCF using:
Bgzip-compressed and tabix-indexed file with annotations. The filecan be VCF, BED, or a tab-delimited file with mandatory columns CHROM, POS(or, alternatively, FROM and TO), optional columns REF and ALT, and arbitrarynumber of annotation columns. BED files are expected to havethe ".bed" or ".bed.gz" suffix (case-insensitive), otherwise a tab-delimited file is assumed.Note that in case of tab-delimited file, the coordinates POS, FROM and TO areone-based and inclusive. When REF and ALT are present, only matching VCFrecords will be annotated. If the END coordinate is present in the annotation fileand given on command line as "-c INFO/END", then VCF records will be matched also by the INFO/END coordinate.If ID is present in the annotation file and given as "-c ID", then VCF records will be matchedalso by the ID column. When multiple ALT alleles are present in the annotation file (given ascomma-separated list of alleles), at least one must match one of thealleles in the corresponding VCF record. Similarly, at least onealternate allele from a multi-allelic VCF record must be present in theannotation file. Missing values can be added by providing "." in place of actual valueand using the missing value modifier with -c, such as ".TAG". Note that flag types, such as "INFO/FLAG", can be annotated by includinga field with the value "1" to set the flag, "0" to remove it, or "." tokeep existing flags.See also -c, --columns and -h, --header-lines.
Comma-separated list of columns or tags to carry over from the annotation file(see also -a, --annotations). If the annotation file is not a VCF/BCF,list describes the columns of the annotation file and must include CHROM,POS (or, alternatively, FROM and TO), and optionally REF and ALT. Unusedcolumns which should be ignored can be indicated by "-". If the annotation file is a VCF/BCF, only the edited columns/tags must be present and theirorder does not matter. The columns ID, QUAL, FILTER, INFO and FORMATcan be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".The imported VCF annotations can be renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG". To carry over all INFO annotations, use "INFO". To add all INFO annotations except"TAG", use "^INFO/TAG". By default, existing values are replaced. By default, existing tags are overwritten unless the source value is a missing value (i.e. ".").If also missing values should be carried over (and overwrite existing tags), use ".TAG" instead of "TAG".To add annotations without overwriting existing values (that is, to add tags that are absent orto add values to existing tags with missing values), use "+TAG" instead of "TAG". These can be combined,for example ".+TAG" can be used to add TAG even if the source value is missing but only if TAG does notexist in the target file; existing tags will not be overwritten.To append to existing values (rather than replacing or leaving untouched), use "=TAG"(instead of "TAG" or "+TAG").To replace only existing values without modifying missing annotations, use "-TAG".To match the record also by ID or INFO/END, in addition to REF and ALT, use "ID" or "INFO/END".If position needs to be replaced, mark the column with the new position as "POS". If the annotation file is not a VCF/BCF, all new annotations must bedefined via -h, --header-lines. See also the -l, --merge-logic option.
Read the list of columns from a file (normally given via the -c, --columns option)."-" to skip a column of the annotation file.One column name per row, an additional space- or tab-separated field canbe present to indicate the merge logic (normally given via the -l, --merge-logic option).This is useful when many annotations are added at once.
When multiple regions overlap a single record, this option defines how to treat multipleannotation values when setting tag in the destination file: use the first encountered value ignoringthe rest (first); append allowing duplicates (append); append even if the appended value is missing,i.e. is a dot (append-missing); append discarding duplicate values (unique);sum the values (sum, numeric fields only); average the values (avg); use the minimum value (min) orthe maximum (max).+Note that this option is intended for use with BED or TAB-delimited annotation files only. Moreover,it is effective only when either REF and ALT or BEG and END --columns are present .+Multiple rules can be given either as a comma-separated list or giving the option multiple times.This is an experimental feature.
minimum overlap required as a fraction of the variant in the annotation -a file (ANN), in thetarget VCF file (:VCF), or both for reciprocal overlap (ANN:VCF).By default overlaps of arbitrary length are sufficient.The option can be used only with the tab-delimited annotation -a file and with BEG and ENDcolumns present.
by default, all samples are assumed to come from a single population. This option allows to group samplesinto populations and apply the HWE assumption within but not across the populations. FILE is a tab-delimitedtext file with sample names in the first column and group names in the second column. If - isgiven instead, no HWE assumption is made at all and single-sample calling is performed. (Note thatin low coverage data this inflates the rate of false positives.) The -G option requires the presence ofper-sample FORMAT/QS or FORMAT/AD tag generated with bcftools mpileup -a QS (or -a AD).
Concatenate or combine VCF/BCF files. All source files must have the same samplecolumns appearing in the same order. Can be used, for example, toconcatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indelVCF into one. The input files must be sorted by chr and position. The filesmust be given in the correct order to produce sorted VCF on output unlessthe -a, --allow-overlaps option is specified. With the --naive option, the filesare concatenated without being recompressed, which is very fast..
convert IMPUTE2 output to VCF. One of the ID columns ("SNP ID" or "rsID" in -genomics.org/plink/2.0/formats#gen) must be of the form"CHROM:POS_REF_ALT" to detect possible strand swaps. When the --vcf-ids option is given, the other column (autodetected) is usedto fill the ID column of the VCF. See also -g and --3N6 options. 2ff7e9595c
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