How Exactly Is Qual Calculated In A Vcf File?

Question

[Tomáš Beluský]

I found some similar topics here and also on another forums, but I still don't know how to exactly calculate quality for each variation in VCF file.

Thanks for all your help!

[lh3]

For samtools and GATK, read the samtools paper. EDIT: Er.. autolink is breaking my link.

[Istvan Albert]

sorry about that - I changed the regexp - the error that you hit should be handled although others may creep up so I'll be watching to see if this causes more trouble than good

Answer 1

[Istvan Albert]

I am going just add this to improve our answered question statistics ;-)

As lh3 says the samtools paper has the answer