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Concatenated fastq files to vcf format


I have had blood samples of a dozen patients with breast cancer.
Each sample was sequenced several times. And so there is several
FASTQ-files for the each sample. Next, the files corresponding to the
same sample were concatenated.
As a result, I have FASTQ-file size of about 30-40 GB per sample.
Is it possible to convert such data to the VCF format using samtools?
I want to do this in order to analyze the VCF files subsequently.

Could you advise how to handle my data? I would be very grateful to you.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Creating a VCF is not a simple format conversion, it involves data analysis. Please see our Best Practices documentation for guidance, as well as the Presentations section for overview videos.
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