Galaxy |

Intersect (version 1.0.0)

First VCF file:

intersect with file of format:

second VCF file:

Priority file:

If the priority file argument is set (this must be equal to one of the input vcf files), then the record written to the output will come from this file. If this argument is not set, the record with the highest quality is written out.

What it does

This tool uses vcfPytools' intersect command to generate the intersection of two VCF files

Two input files are required as input and the intersection of these two files is generated and sent to the output. These files must be sorted by genomic coordinate to function correctly, although the reference sequence order is no important.

The intersection can be calculated on two VCF files or a VCF and a BED file.

If the priority file argument is set (this must be equal to one of the input VCF files), then the record written to the output will come from this file. If this argument is not set, the record with the highest quality is written out.