[wdt]

Hello,

Could someone please provide more description of each field in the info string?

DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 39,6,0:1/1:49

I know that DP is depth of coverage. What are AF1, CI95 (confidence interval?), DP4?

Are 39,6,0 showing AA:AB:BB (guess)? Then should they be related to to the DP value?

For multiple sample case, is there a way to find allelic frequency for each
sample using the INFO field? Can someone show an example?





The documentation on VCF4.0 http://www.1000genomes.org/wiki/Anal...mat-version-40

seems to have skipped the explanation for these fields.

Any help with this will be most appreciated. Thanks all, this is a terrific forum.

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I found the answers at http://samtools.sourceforge.net/mpileup.shtml. It is well-explained there.

[cboustred]

Hi wdt, see http://samtools.sourceforge.net/mpileup.shtml for a description of the fields.

I'm a newbie to all this NGS business so cannot expand on what they all mean, I'm slowly trying to work it out for myself!

Good luck