htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing

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vcf2adam unparsable vcf record

The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing

Ambiguity codes on reference

The provided VCF file is malformed at approximately line number 108: unparsable vcf record with allele S, for input source: /media/TeraData/ipedroso/ANALYSES/DEKKERA/variation/AWRI1499_ref/awri1499_vsawri1499Ref/work/freebayes/AWRI1499_contig1_scaffold1/1-AWRI1499_contig1_scaffold1_0_12137.vcf.gz

SV pipeline: missing alleles makes VCF sorting crash

The provided VCF file is malformed at approximately line number 88: empty alleles are not permitted in VCF records

Malformed VarDict VCF file crashes GATK and pipeline

The provided VCF file is malformed at approximately line number 54693: BUG: log10PError cannot be > 0 : 1.0, for input source: /pico/scra tch/userexternal/esebesty/bcbio_run/uuid_batch5932/work/vardict/21/LUAD_5932-21_0_41399576.vcf.gz

CatVariant not handling allele "*" in gatk-haplotype-joint

The provided VCF file is malformed at approximately line number 649: unparsable vcf record with allele *, for input source: /media/jawhite/Data/662-exome-trio/work/joint/gatk-haplotype-joint/trio-bwa-j/1/trio-bwa-j-1_0_15543565.vcf.gz

Investigate failures to load ExAC.0.3.GRCh38.vcf variants

The provided VCF file is malformed at approximately line number 15364: Duplicate allele added to VariantContext: C

htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1787: The reference allele cannot be missing	at htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:783)	at htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:572)	at htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:531)	at htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:336)	at htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:279)	at htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:257)	at org.seqdoop.hadoop_bam.VCFRecordReader.nextKeyValue(VCFRecordReader.java:144)	at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:163)	at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)	at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply$mcV$sp(PairRDDFunctions.scala:1034)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply(PairRDDFunctions.scala:1034)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12$$anonfun$apply$4.apply(PairRDDFunctions.scala:1034)	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1206)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1042)	at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1014)	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)	at org.apache.spark.scheduler.Task.run(Task.scala:88)	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)	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)