Hi there,
I am exploring freebayes for SNP calling. It works nicely and the next step will be to filter the SNPs based on quality, etc., but I am a little confused about how to interpret the QUAL value in the freebayes *.vcf.
In standard VCF format the QUAL is phred scaled, right, so a QUAL value of 30 means a probability of 0.001 that the SNP is called incorrectly.
The freebayes QUAL values are in the range of some hundred to several thousand. Can anyone tell me how to interpret that?
much obliged!!!
I am exploring freebayes for SNP calling. It works nicely and the next step will be to filter the SNPs based on quality, etc., but I am a little confused about how to interpret the QUAL value in the freebayes *.vcf.
In standard VCF format the QUAL is phred scaled, right, so a QUAL value of 30 means a probability of 0.001 that the SNP is called incorrectly.
The freebayes QUAL values are in the range of some hundred to several thousand. Can anyone tell me how to interpret that?
much obliged!!!
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