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plagnollab / DNASeq_pipeline

Pipeline in place at the UGI for DNA level analysis
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Post VEP processing bug #33

Closed APLevine closed 9 years ago

APLevine commented 9 years ago

/cluster/project8/IBDAJE/batches_from_uclex/familyB/VEP_16.vcfout

16      50763778        rs5743293       G       GC      199466  .       BaseQRankSum=-0.231;ClippingRankSum=-0.107;DB;DP=105255;FS=0.531;InbreedingCoeff=0.0747;MLEAC=213;MLEAF=0.026;MQ=70;MQ0=0;MQRankSum=0.243;QD=14.44;ReadPosRankSum=-0.466;AC=17;AN=64;CSQ=C|ENSG00000167207|ENST00000300589|Transcript|frameshift_variant|3121-3122|3016-3017|1006|A/AX|gcc/gCcc|rs2066847||1|NOD2|HGNC|5331|YES|||C:0.0078|C:0.01|C:0.01||C:0.01|C:0.004690|C:0.022171||||||;UCLEX=G>GC:0.0164993;EXAC_Adj=G>GC:0.01305724;EXAC_AFR=G>GC:0.00269283;ESP_EA=G>GC:0.0221710685728;EXAC_EAS=G>GC:0.00046232;EXAC_OTH=G>GC:0.00550661;EXAC_NFE=G>GC:0.02016552;EXAC_AMR=G>GC:0.00684813;ESP_AA=G>GC:0.0046904315197;EXAC_SAS=G>GC:0.00151442;EXAC_FIN=G>GC:0.01482154

This variant is not represented correctly in the -annotations.csv file:

/cluster/project8/IBDAJE/batches_from_uclex/familyB/VEP_16-annotations.csv

16_50763778_G_GC,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.00269283,0.00684813,0.01305724,0.00046232,0.01482154,0.02016552,0.00550661,0.00151442,0.0164993,NA,NA,NA,NA,0.0221710685728,0.0046904315197,0.25,16.0,15.0,1.0,2.0
pontikos commented 9 years ago

I was not stripping the ref allele from an insertion. This has now been corrected:

16_50763778_G_GC,rs5743293,C,ENSG00000167207,ENST00000300589,Transcript,frameshift_variant,3121-3122,3016-3017,1006,A/AX,gcc/gCcc,rs2066847,,1,NOD2,HGNC,5331,YES,,,,,,,,,NA,NA,NA,NA,NA,NA,NA,NA,0.00269283,0.00684813,0.01305724,0.00046232,0.01482154,0.02016552,0.00550661,0.00151442,0.0164993,NA,NA,NA,NA,0.0221710685728,0.0046904315197,0.25,16.0,15.0,1.0,2.0