https://github.com/lindenb/htsplusplus
Select variants from VCF/BCF spaced by a distance 'd'.
https://github.com/lindenb/htsplusplus
bcf bioinformatics c distance htslib variants vcf
Last synced: about 1 month ago
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Select variants from VCF/BCF spaced by a distance 'd'.
- Host: GitHub
- URL: https://github.com/lindenb/htsplusplus
- Owner: lindenb
- License: mit
- Created: 2020-12-03T08:29:35.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2024-11-18T20:14:14.000Z (over 1 year ago)
- Last Synced: 2026-02-12T07:52:44.969Z (4 months ago)
- Topics: bcf, bioinformatics, c, distance, htslib, variants, vcf
- Language: C++
- Homepage:
- Size: 303 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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.