Does Nextera Transposase adapter sequence affects GATK HaplotypeCaller pipeline?

Question

[Susmita Mandal]

Hi,

I trimmed my paired end fastq data using Trimmomatic using TruSeq-PE adapters, but actually they contain Nextera transposase adapter sequences. I have already aligned and did variant calling using GATK "HaplotypeCaller". Would the adapter contamination will affect the variant calling?

Please help me out.

Thanks,

Susmita

[ATpoint]

How many reads are affected? Run fastqc on the bam files to find out.