Question: How Exactly Is Qual Calculated In A Vcf File?
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gravatar for Tomáš Beluský
6.3 years ago by
Brno
Tomáš Beluský90 wrote:

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 • 3.0k views
ADD COMMENTlink modified 6.3 years ago by Istvan Albert ♦♦ 80k • written 6.3 years ago by Tomáš Beluský90

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

ADD REPLYlink modified 6.3 years ago by Istvan Albert ♦♦ 80k • written 6.3 years ago by lh331k

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 REPLYlink written 6.3 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Istvan Albert
6.3 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

As lh3 says the samtools paper has the answer

ADD COMMENTlink written 6.3 years ago by Istvan Albert ♦♦ 80k
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