| BCFtools is a program for variant calling and manipulating VCFs and BCFs. It replaces the original samtools BCF calling from the bcftools subdirectory of samtools, and renders obsolete most of the perl VCFtools. |
hg clone https://testtoolshed.g2.bx.psu.edu/repos/wrtz/bcftools
| Repository package_zlib_1_2_8 revision 3348f1acee2a owned by iuc (prior install required) |
| Repository package_ncurses_5_9 revision ad27910a950c owned by iuc (prior install required) |
| Repository package_zlib_1_2_8 revision 3348f1acee2a owned by iuc (prior install required) |
| Repository package_tabix_0_2_6 revision 54f8b9bf9b6c owned by iuc (prior install required) |
| Name | Version | Type | |
|---|---|---|---|
| bcftools | 1.3 | package | |
| samtools | 1.2 | package | |
| tabix | 0.2.6 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Modify header of VCF/BCF files, change sample names | 1.0.0 | any | |
| Left-align and normalize indels, check if REF alleles match reference, change multiallelic format | 1.0.0 | any | |
| Index tab-delimited file | 1.0.0 | any | |
| Add or remove annotations | 1.0.0 | any | |
| Run bgzip compression on file | 1.0.0 | any | |
| Convert, view, subset, and filter VCF/BCF files | 1.0.0 | any | |
| Merge multiple VCF/BCF files | 1.0.0 | any | |
| Index FASTA file using samtools faidx command | 1.0.0 | any | |
| Apply fixed-threshold filters | 1.0.0 | any | |
| Output VCF/BCF fields in user-defined format | 1.0.0 | any | |