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08-10-2011, 02:57 PM
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Senior Member
Location: IL Join Date: Jul 2011
Posts: 100
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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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