Does Nextera Transposase adapter sequence affects GATK HaplotypeCaller pipeline?
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
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Susmita Mandal
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How many reads are affected? Run
fastqcon the bam files to find out.