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Need some suggestions

Sir,
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.
Best Regards
Zillur

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @zillurbmb51
    Hi Zillur,

    Can you tell us a little more about how you processed your samples? Did you follow GATK Best Practices? Do you have one whole genome or one whole exome? If you are working with non-human data, is the Ti/Tv ration known to be lower in your organism?

    Thanks,
    Sheila

  • zillurbmb51zillurbmb51 USAMember

    Thank you very much fro your kind reply. I have downloaded paired-end fast files from: http://www.ebi.ac.uk/ena/data/view/Taxon:5864&portal=read_experiment&subtree=true
    Then I aligned them using BOWTIE2 against fasta assembly, then sorted, pileup the bam file using SAMTOOLS and then used BCFTOOLS. But my Ts/Tv ratio was less then 1.(Maybe for background noise)
    I need to process the datasets(using GATK) for getting a higher Ts/Tv (at least >2) for further analysis(Some peers got ). I will also analyse other genomes of Apecomplexan.
    I did not start the best practice but if you suggest I am going to start. Maybe non-human datasets give a lower Ts/Tv but not lower than 2.

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