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Old 04-30-2015, 01:56 PM   #1
BhariD
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Location: Georgia

Join Date: Mar 2013
Posts: 15
Default Varscan2 multi-variant samples VCF output with empty sample call FORMAT column?

Hi

I have Varscan2 generated multi-sample (three samples total) variant VCF file.
I ran Varscan2 on default settings.

For few variants, there is no variant call FORMAT string (e.g., "0/1:2:11:." ) for the third sample, it is completely empty; however for the first two samples there is a variant FORMAT string.

Does anyone know what is the reason for an empty FORMAT specific to a sample in Varscan2 output? is it the read depth?

Thank you.

Regards,
BD
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