Pedigree Analysis
Posted in Ask the GATK team | Last updated on 2013-07-17 04:35:31


Comments (18)

Hi,

I am trying to use PED files when I run UnifiedGeotyper, variantannotator and VariantRecalibrator (The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14)

if I don't add the PED file , I have some InbreedingCoeff

annotation=[SnpEff, AlleleBalance, BaseCounts, GCContent, HardyWeinberg, IndelType, AlleleBalanceBySample, MappingQualityZeroBySample]

1       14653   .       C       T       22.54   LowQual ABHet=0.842;ABHom=0.803;AC=4;AF=0.182;AN=22;BaseCounts=1,1362,0,261;BaseQRankSum=-4.292;DP=1075;Dels=0.00;FS=4.692;GC=58.42;HW=2.5;HaplotypeScore=0.0000;InbreedingCoeff=0.0530;MLEAC=3;MLEAF=0.136;MQ=6.41;MQ0=967;MQRankSum=-2.246;OND=0.164;QD=0.08;ReadPosRankSum=-0.008;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=DDX11L1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000456328;set=FilteredInAll      GT:AB:AD:DP:GQ:MQ0:PL

but when I add the PED file, I have nothing

annotation=[AlleleBalance, BaseCounts, GCContent, HardyWeinberg, IndelType, AlleleBalanceBySample, MappingQualityZeroBySample, InbreedingCoeff] pedigree=[/scratch/cbrc/data/release_2012_Nov/BostonHF/PED/BostonHF.ped] pedigreeString=[] pedigreeValidationType=SILENT

1       14653   .       C       T       10.43   LowQual ABHom=0.792;AC=2;AF=0.091;AN=22;BaseCounts=1,1362,0,261;BaseQRankSum=-3.828;DP=1075;Dels=0.00;FS=2.373;GC=58.42;HW=10.2;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.045;MQ=6.20;MQ0=976;MQRankSum=-2.768;OND=0.190;QD=0.10;

and my PED file seems is bad format because I have this message

INFO  17:02:17,687 PedReader - Reading PED file /scratch/cbrc/data/release_2012_Nov/BostonHF/PED/BostonHF.ped with missing fields: [] 
INFO  17:02:17,687 PedReader - Reading PED file /scratch/cbrc/data/release_2012_Nov/BostonHF/PED/BostonHF.ped with missing fields: [] 
INFO  17:02:17,687 PedReader - Reading PED file /scratch/cbrc/data/release_2012_Nov/BostonHF/PED/BostonHF.ped with missing fields: [] 
INFO  17:02:17,687 PedReader - Reading PED file /scratch/cbrc/data/release_2012_Nov/BostonHF/PED/BostonHF.ped with missing fields: [] 
INFO  17:02:17,770 PedReader - Phenotype is other? false 
INFO  17:02:17,770 PedReader - Phenotype is other? false 
INFO  17:02:17,770 PedReader - Phenotype is other? false 
INFO  17:02:17,775 PedReader - Phenotype is other? false 

But I have 6 columns and the name and tabulation between each column

2 MN932002 0 0 2 1
2 PNB32015 0 MN932002 1 1
4 CS934001 0 0 2 2
4 RMAO8004 0 CS934001 1 2
6 KH948045 0 0 2 2
6 AHAO8001 0 0 2 2
6 MHAO8003 0 0 2 2
A LSB32012 0 0 2 2
A SBB32010 0 LSB32012 2 2
B CMSB32011 0 0 2 2
C MKB32014 0 0 2 2
Z M88BBTPL 0 0 other -9

for the phenotype :

-9 missing 1 unaffected 2 affected

Consequently, I cannot run " VariantRecalibrator with -an InbreedingCoeff". Could you help me ?

Thanks,

Tiphaine


Return to top Comment on this article in the forum