Try to find the strand_bias_counts definition?

[ipstone]

Hello,

We would like to find the stand_bias information in mutect output. Currently we are using mutect 1.1.7 version, and there is a stand_bias_count field in the output.

An example of stand_bias_counts is like:
(117,114,7,7)

We assumed that it might be:

• the reference allele on the forward strand
• the reference allele on the reverse strand
• the alternate allele on the forward strand
• the alternate allele on the reverse strand

But the numbers don't add up to read depth field.
It would be very helpful if someone can tell the definition of this field, or where we can find the strand information for the mutant allele call etc. Thanks

Searching the source code, we found something might be relevant:
candidate.setStrandContingencyTable(SequenceUtils.getStrandContingencyTable(forwardPileup, reversePileup, (byte) upRef, (byte) altAllele));
but what is the deinfition of the forwardPileup, reversePileup, (byte) upRef, (byte) altAllele ?

Really appreciate any help and suggestions!