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Old 08-10-2011, 02:57 PM   #1
shuang
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Location: IL

Join Date: Jul 2011
Posts: 100
Default 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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