Why Penncnv Calcuate Baf As 2 For Some Markers

Question

[User 0559]

Hello Biostars,

I am sorry if my question is embarrassingly easy. I was trying to use pennCNV to estimate LRR and BAF in a group of 130 samples. However, the BAF for a lot of the markers (approximately 50%) was reported to be 2, which doesn't seem to be reasonable to me. Did anyone encounter this problem before?

The code I used to generate the results are as follows:

~/penncnv/gw6/bin/normalizeaffygenocluster.pl \ ~/step7genocluster\ ~/quant-norm.pm-only.med-polish.expr.summary.txt \ --locfile ~/enncnv/gw6/lib/affygw6.hg19.pfb \ --output ~/step8lrrbaf.txt \

Thank you very much!I really appreciate any advise.

Answer 1

[Austinlew]

Affy6 chip contains 900k non-polymorphic probes for copy number detection in addition to 900k SNP probes, so BAF of 50% (non-polymorphic probes) are 2 .