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Test-drive the GATK tools and Best Practices pipelines on Terra
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Need some suggestions
Hope this mail will find you in sound. I was trying to analyse paired-end B.microti genome using BOWTIE2, SAMTOOLS, BCFTOOLS. I got a good 'Q' value in FASTQC, a very good alignment rate (~70-90%) and high sequence coverage/depth all of which suggests a very high quality of the sequence. But I got a relatively low Ts/Tv value (<1) which is unusual. Some of mentors told me that using GATK will give me higher Ts/Tv ratio. Would you please to give me some hints about this matter.