Importance of lane information in Picard and GATK

[MurielGB]

Hello,

I have several individuals sequenced with Illumina and I want to make variant calling.
Each individuals was sequenced in 3 lanes.

I was wondering if the lane information (stored in RG) is important for the GATK workflow or not ?

This is because I could used the merged file of all lanes for mapping instead of doing 3 mappings because I have 3 lanes, add the lane info and then merge.

Thanks !

Muriel

[lindenb]

It's important in the gatkwhen you use Reads filters like "PlatformUnitFilter" ( http://www.broadinstitute.org/gatk/s...formUnitFilter )