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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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P-values to de novo CNV calls #12

Closed ThaFG closed 7 years ago

ThaFG commented 7 years ago

Hi, After identifying the new CNVs by Joint I did the assigning P-values to new CNV calls (validating predicted new CNVs)

But some results (p-value) are strange, they are greater than 1. My code and result obtained (pvalor of 1.5) follows below. I hope you can help me. 

infer_snp_allele.pl -pfb allsamples.pfb -hmm Test.hmm -denovocn 3 FATHER.txt MOTHER.txt     SON.txt -start SNPX1 -end SNPX2 -out tempfile

... [7] "NOTICE: For the region chr1:38730376-38750794, 12 markers were identified from FATHER.txt"
[8] "NOTICE: For the region chr1:38730376-38750794, 12 markers were identified from MOTHER.txt"
[9] "NOTICE: For the region chr1:38730376-38750794, 12 markers were identified from SON.txt"
[10] "NOTICE: Analyzing trio FATHER.txt MOTHER.txt SON.txt"
[11] "NOTICE: Evidence for parental origin for the putative de novo CNVs (de novo CN=3 in trio FATHER.txt MOTHER.txt SON.txt ): Marker= 12 Paternal_origin(F)= 1 Maternal_origin(M)= 1 P-value= 1.5"

temfile Name LRR_F LRR_M LRR_O BAF_F BAF_M BAF_O GENO_F GENO_M GENO_O 1 AX-75442315 1.22384240 -0.40021763 0.83387941 0.10771760 0.9991463 0.28033960 AA BB AAB 2 AX-80739365 -0.05270831 -0.17584350 0.47600501 0.00000000 0.0000000 0.01227067 AA AA AAA 3 AX-75442328 -0.37651942 -0.03768277 0.28612970 1.00000000 0.5252890 0.35981647 BB AB AAB 4 AX-80782291 -0.01382187 -0.06273745 0.38581987 0.01677153 0.4654819 0.00000000 AA AB AAA 5 AX-75442339 0.13877110 0.14623184 0.62283328 1.00000000 0.9839616 0.98646505 BB BB BBB 6 AX-80822384 -0.11190325 -0.45343429 -0.08698980 1.00000000 0.1148214 0.25401103 BB AA AAB 7 AX-75442344 -0.08249386 -0.14573546 0.07661979 1.00000000 0.5163739 0.71945969 BB AB ABB 8 AX-75442345 -0.22875525 -0.19777528 0.28132614 0.95536751 1.0000000 1.00000000 BB BB BBB 9 AX-75442350 0.01422247 -0.08666986 0.17382427 0.00000000 1.0000000 0.34468498 AA BB AAB 10 AX-75442353 -0.02782679 -0.12583260 0.09268115 0.97720128 0.9691261 0.95098485 BB BB BBB 11 AX-80762445 0.04548795 -0.51386653 0.54591703 0.99233125 0.1648574 0.45089455 BB NC AAB 12 AX-75442357 0.06765128 0.07259621 0.41891134 0.99409324 1.0000000 0.96811810 BB BB BBB Origin 1 ? 2 ? 3 M 4 ? 5 ? 6 ? 7 F 8 ? 9 ? 10 ? 11 ? 12 ?

I look forward to hearing from you.

kaichop commented 7 years ago

issue fixed and closed.