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-   -   Varscan2 multi-variant samples VCF output with empty sample call FORMAT column? (http://seqanswers.com/forums/showthread.php?t=58167)

BhariD 04-30-2015 01:56 PM

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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