diff --git a/howtos/FAQ.html b/howtos/FAQ.html index 1237d6d5..f646b1d4 100644 --- a/howtos/FAQ.html +++ b/howtos/FAQ.html @@ -110,7 +110,7 @@

Frequently Asked Questions

-

The error above is printed when different number of values is encoutered, for example AC=1 or AC=1,1,1 in the example above.

+

The error above is printed when different number of values is encountered, for example AC=1 or AC=1,1,1 in the example above.

Other such definitions are Number=R (there must be as many values as there are REF+ALT alleles in total), diff --git a/howtos/FAQ.txt b/howtos/FAQ.txt index ffbd3e39..279a982d 100644 --- a/howtos/FAQ.txt +++ b/howtos/FAQ.txt @@ -20,7 +20,7 @@ and expects a value for each ALT allele, for example ---- chr1 64334 . A C,T . . AC=1,1 GT 0/1 0/1 ---- -The error above is printed when different number of values is encoutered, for example `AC=1` or `AC=1,1,1` in the example above. +The error above is printed when different number of values is encountered, for example `AC=1` or `AC=1,1,1` in the example above. Other such definitions are `Number=R` (there must be as many values as there are REF+ALT alleles in total), and `Number=G` (this is more complicated, see the section 1.4.2 of the link:http://samtools.github.io/hts-specs/VCFv4.3.pdf[VCF specification]). diff --git a/howtos/bcftools.txt b/howtos/bcftools.txt index 71ea2901..8f99d80a 100644 --- a/howtos/bcftools.txt +++ b/howtos/bcftools.txt @@ -408,7 +408,7 @@ Add or remove annotations. # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive) tabix -s1 -b2 -e3 annots.tab.gz - bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf + bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals) bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf @@ -1022,7 +1022,7 @@ See the usage examples below. # %TBCSQ .. print consequences in both haplotypes in separate columns # %TBCSQ{0} .. print the first haplotype only # %TBCSQ{1} .. print the second haplotype only - # %TBCSQ{*} .. print a list of unique consquences present in either haplotype + # %TBCSQ{*} .. print a list of unique consequences present in either haplotype bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf ---- @@ -2069,7 +2069,7 @@ Extracts fields from VCF or BCF files and outputs them in user-defined format. %SAMPLE Sample name %POS0 POS in 0-based coordinates %END End position of the REF allele - %END0 End position of the REF allele in 0-based cordinates + %END0 End position of the REF allele in 0-based coordinates \n new line \t tab character diff --git a/howtos/cnv-calling.html b/howtos/cnv-calling.html index 8e3bd529..8438c19b 100644 --- a/howtos/cnv-calling.html +++ b/howtos/cnv-calling.html @@ -181,7 +181,7 @@

Detecting subchromosomal CNVs

-
bcftools cnv -c conrol_sample -s query_sample -o outdir/ -p 0 file.vcf
+
bcftools cnv -c control_sample -s query_sample -o outdir/ -p 0 file.vcf
diff --git a/howtos/cnv-calling.txt b/howtos/cnv-calling.txt index e6437c2e..4a40ab3b 100644 --- a/howtos/cnv-calling.txt +++ b/howtos/cnv-calling.txt @@ -81,7 +81,7 @@ differences between two samples. This greatly helps to reduce the number of false calls and also allows one to distinguish between normal and novel copy number variation. The command is ---- -bcftools cnv -c conrol_sample -s query_sample -o outdir/ -p 0 file.vcf +bcftools cnv -c control_sample -s query_sample -o outdir/ -p 0 file.vcf ---- The ``-p 0`` option tells the program to automatically call matplotlib and produce plots like the one in this example: diff --git a/howtos/index.html b/howtos/index.html index 64d2b813..adc2d9d7 100644 --- a/howtos/index.html +++ b/howtos/index.html @@ -97,7 +97,7 @@

About BCFtools

BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. -In order to avoid tedious repetion, throughout this document we will use +In order to avoid tedious repetition, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted.

diff --git a/howtos/index.txt b/howtos/index.txt index 7318b68d..de8ed53e 100644 --- a/howtos/index.txt +++ b/howtos/index.txt @@ -15,7 +15,7 @@ https://github.com/samtools/bcftools/issues[github]. BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. -In order to avoid tedious repetion, throughout this document we will use +In order to avoid tedious repetition, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted. Most commands accept VCF, bgzipped VCF and BCF with filetype detected diff --git a/howtos/plugin.fixref.html b/howtos/plugin.fixref.html index 10ae8a3c..1d95e8de 100644 --- a/howtos/plugin.fixref.html +++ b/howtos/plugin.fixref.html @@ -155,7 +155,7 @@

Plugin fixref

In the most extreme case when nothing else is working, one can simply force -the unambigous alleles onto the forward strand and drop the ambigous genotypes.

+the unambiguous alleles onto the forward strand and drop the ambiguous genotypes.

diff --git a/howtos/plugin.fixref.txt b/howtos/plugin.fixref.txt index b5997e03..58a68f78 100644 --- a/howtos/plugin.fixref.txt +++ b/howtos/plugin.fixref.txt @@ -54,7 +54,7 @@ bcftools sort fixref.bcf -Ob -o fixref.sorted.bcf In the most extreme case when nothing else is working, one can simply force -the unambigous alleles onto the forward strand and drop the ambigous genotypes. +the unambiguous alleles onto the forward strand and drop the ambiguous genotypes. ---- bcftools +fixref test.bcf -Ob -o output.bcf -- -f ref.fa -m flip -d ---- diff --git a/howtos/query.html b/howtos/query.html index 79a9d64a..e6b92241 100644 --- a/howtos/query.html +++ b/howtos/query.html @@ -111,7 +111,7 @@

Extracting information from VCFs

-

In this example, the -f otion defines the output format. The %POS string +

In this example, the -f option defines the output format. The %POS string indicates that for each VCF line we want the POS column printed. The \n stands for a newline character, a notation commonly used in the world of computer programming. Any characters without a special meaning diff --git a/howtos/query.txt b/howtos/query.txt index d4ba4fee..a2bff8bb 100644 --- a/howtos/query.txt +++ b/howtos/query.txt @@ -25,7 +25,7 @@ bcftools query -l file.bcf | wc -l ---- bcftools query -f '%POS\n' file.bcf ---- -In this example, the `-f` otion defines the output format. The `%POS` string +In this example, the `-f` option defines the output format. The `%POS` string indicates that for each VCF line we want the POS column printed. The `\n` stands for a newline character, a notation commonly used in the world of computer programming. Any characters without a special meaning diff --git a/howtos/roh-calling.html b/howtos/roh-calling.html index 5a7d71f1..8bb6f77f 100644 --- a/howtos/roh-calling.html +++ b/howtos/roh-calling.html @@ -230,7 +230,7 @@

Troubleshooting

-

If the number of the processed sites is too low, check what was the reason for exluding +

If the number of the processed sites is too low, check what was the reason for excluding them. This command should give the number of sites that were processed:

@@ -262,4 +262,4 @@

Feedback

- \ No newline at end of file + diff --git a/howtos/roh-calling.txt b/howtos/roh-calling.txt index f3c46351..344cb887 100644 --- a/howtos/roh-calling.txt +++ b/howtos/roh-calling.txt @@ -148,7 +148,7 @@ program. For example in this run many sites were filtered: Number of lines: total/processed: 599218/37730 ---- -If the number of the processed sites is too low, check what was the reason for exluding +If the number of the processed sites is too low, check what was the reason for excluding them. This command should give the number of sites that were processed: ----