Question

How Exactly Is Qual Calculated In A Vcf File?

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11.7 years ago

Tomáš Beluský ▴ 90

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!

vcf • 4.4k views

ADD COMMENT • link updated 11.7 years ago by Istvan Albert 102k • written 11.7 years ago by Tomáš Beluský ▴ 90

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

ADD REPLY • link updated 11.7 years ago by Istvan Albert 102k • written 11.7 years ago by lh3 33k

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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

ADD REPLY • link 11.7 years ago by Istvan Albert 102k

score 0 · Answer 1 · 2013-03-24

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11.7 years ago

Istvan Albert 102k

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

As lh3 says the samtools paper has the answer

ADD COMMENT • link 11.7 years ago by Istvan Albert 102k