Description

Split VCF by sample, creating single- or multi-sample VCFs.

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

samples (file)

A tab-separated file determining which samples should be in which output file column 1: The sample name(s) in the input file column 2: The sample name(s) to use in the output file (use - to keep the original name) column 3: The name of the output file Either this or a groups file should be given

*

groups (file)

A tab-separated file determining which samples should be in which output file(s) column 1: The sample name(s) in the input file column 2: The sample name(s) to use in the output file (use - to keep the original name) column 3: The name of the output file(s) Either this or a samples file should be given

*

regions (file)

A BED file containing regions to use

*.bed

targets (file)

A BED file containing regions to use (but streams rather than index-jumps)

*.bed

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

Tools

pluginsplit Documentation

Split VCF by sample, creating single- or multi-sample VCFs.

doi: 10.1093/bioinformatics/btp352License: MIT
Authors