lindenb / htsplusplus

Select variants from VCF/BCF spaced by a distance 'd'.

hts++

Compilation

compilation requires a C++ compiler and xsltproc.

git clone "https://github.com/lindenb/htsplusplus"

autoconf -Wno-syntax
./configure --with-htslib= --with-htslib=${PWD}/../htslib    # see ./configure --help and samtools's INSTALL
make

subcommands

SAMVIEWWITHMATE

select read and their mate that falls within a region from a query sorted BAM

Usage

hts++ samviewwithmate [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
-R	--reference		FASTA reference
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--bam-output-format		output format for sam: SAM, BAM, CRAM
-@	--nthreads		Number of threads
-i	--inverse		inverse logic: keep read where no read in the pair overlap the BED file
-B	--bed		A BED file.

BCFPRUNE

Select variants with a fixed distance in a VCF file.

Usage

hts++ bcfprune [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--vcf-output-format		output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v)
-d	--distance		distance

BCFCONCAT

concatenanate multiple vcf/bcf files

Usage

hts++ bcfconcat in1.bcf in2.vcf.gz in3.vcf
hts++ bcfconcat bcfs.list
cat bcfs.list | hts++ bcfconcat

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--vcf-output-format		output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v)

BCFFILTERGT

Select variant using an expression

Usage

hts++ bcffiltergt [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--vcf-output-format		output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v)
-F	--soft-filter		soft FILTER name. (default: filter out variants)
-e	--expression		Expression as string
-f	--file-expression		Expression as file

BCFHEAD

Show the first 'N' variants in a VCF

Usage

hts++ bcfhead [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--vcf-output-format		output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v)
-n	--count		Number of variants

BCF2INTERVALS

convert VCF/BCF to interval of variants that are distant from 'x' bases.

Usage

hts++ bcf2intervals [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
-d	--distance_per_interval		distance
-m	--min-distance		min distance

SAMRMDUPNAMES

remove duplicated names in sorted BAM (prevent graphtyper from failing)

Usage

hts++ samrmdupnames [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
-R	--reference		FASTA reference
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--bam-output-format		output format for sam: SAM, BAM, CRAM
-@	--nthreads		Number of threads

FASTQSPLITNFILES

Split FASTQ to N files

Usage

hts++ fastqsplitnfiles [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-o	--output		output or stdout
-p	--prefix		output prefix
-n	--count-files		number of files
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)

BCFSTREAMUNTIL

Stream a VCF until a position is found.

Usage

hts++ bcfstreamuntil [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
	--compression-level	<0-9>	compression-level 0 (low compression) to 9 (best compression)
-O	--vcf-output-format		output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v)
-o	--output		output or stdout
-p	--position		stop after this position. syntax 'CHROM:POS'

TESTS

peforms some tests

Usage

hts++ tests [options...] (files)

Options

short-option	long-option	argument	description	default-value
-h	--help		Display help and exit
-v	--version		Display Version and exit
-D	--directory		test directory

Author

Pierre Lindenbaum Phd 2022.