java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3

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, 1 year ago
Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3
java.lang.IllegalArgumentException: Multi-allelic site with non-ref symbolic allele[VC Unknown @ chr22:18027817-18027821 Q1364.73 of type=MIXED alleles=[CTTTT*, <NON_REF>, C, CT, CTT, CTTT] attr={DP=78, MLEAC=[0, 0, 1, 1, 0], MLEAF=[0.00, 0.00, 0.500, 0.500, 0.00], MQ=70.00, MQ0=0} GT=GT:AD:DP:GQ:PL:SB 3/4:0,4,6,28,17,0:55:99:1402,1244,2007,972,1382,1297,371,355,301,301,792,617,486,0,653,1038,1016,883,315,597,935:0,0,14,3
at org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:214)
at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1.apply(ADAMContext.scala:823)
at org.apache.spark.util.Utils$.getIteratorSize(Utils.scala:1595)
at org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
at org.apache.spark.rdd.RDD$$anonfun$count$1.apply(RDD.scala:1157)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1858)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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