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3. GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1

Thank you so much for the reply. 

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• Şevval Aktürk
• April 30, 2020 08:31
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3. GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1

I'm sorry I don't have stack trace anymore for 4.1, but I tried with the latest version as you said.  I tried SNP calling from same multiple bam files (low coverage human DNA samples with all the c...

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• Şevval Aktürk
• April 29, 2020 18:57
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3. GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1

Thank you. I searched it in the ALL.chr21.phase3. vcf file ,but it couldn't find that position in chr21. Actually, I tried same command and same input bam file with GATK3 UnifiedGenotyper tool, but...

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• Şevval Aktürk
• April 24, 2020 17:24
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3. GATK4 HaplotypeCaller ERROR : expected haplotypes.size() >= eventsAtThisLoc.size() + 1

Thanks a lot , but I've already used GATK4.1 with same arguments(except min base and mapping quality)  for another bam file. Here is my command: java "-Xmx25g" -jar ..../gatk HaplotypeCaller -I xxx...

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• Şevval Aktürk
• April 23, 2020 16:47
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