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SNP phred-score threshold

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  • SNP phred-score threshold

    A vcf file processed after those 3 commands below seems has filtered low-phred polymorphic bases. What is the default threshold? Where can I change that threshold in command?

    $samtools mpileup -uf Sorbil.fasta sample.bam > sample.pileup

    $bcftools view -bvcg ample.pileup > var.bcf

    $bcftools view var.bcf > var.vcf
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