Special GATK Use Cases
Information here covers items that are not in Best Practices but may someday be a part of Best Practices
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GATK concordance Answered0 votes 22 comments
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java.lang.ArrayIndexOutOfBoundsException: 32772 while running GenotypeGVCFs Answered0 votes 18 comments
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issue while running mitochondrial analysis Answered0 votes 15 comments
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GATK-VQSR issue0 votes 12 comments
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java.lang.ArrayIndexOutOfBoundsException error while using HaplotypeCaller0 votes 12 comments
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"Could not determine local host name" Answered0 votes 12 comments
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no read counts per allele while using gatk ASEReadCounter Answered0 votes 11 comments
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GetPileupSummaries Error: java.lang.OutOfMemoryError: Java heap space Answered0 votes 11 comments
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Best practice for using Mutect2 in serial tumor samples from same patient Answered0 votes 11 comments
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SNP VCF file and bamout not the same Answered0 votes 11 comments
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Mutect2 for RNA-seq?0 votes 11 comments
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Maximum performance HaplotypeCaller Answered1 vote 10 comments
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ASEReadCounter ouputs only header0 votes 10 comments
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Counld I use bam files from HISAT2 to call snp/indels? Answered0 votes 10 comments
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Dealing with spaces in gatk CombineGVCFs file paths0 votes 9 comments
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disable_read_filter function cannot be disabled Answered0 votes 9 comments
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How to run BwaMemIndexImageCreator on large input? Answered0 votes 9 comments
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Mutec2 - Liquid Biopsy0 votes 9 comments
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PathSeq error: java.lang.NumberFormatException0 votes 8 comments
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Monomorphic sites after GenotypeGVCFs --include-non-variant-sites Answered0 votes 8 comments
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--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' Answered0 votes 8 comments
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reads filtered by Mutect2 having MAPQ 25 Answered0 votes 8 comments
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GATK4.0.3.0 GenotypeGVCFs - Could not open array genomicsdbarray0 votes 8 comments
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Mutect2 Calls for non-tumor pooled samples - no variants pass filters0 votes 7 comments
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CombineGVCFs produces .bcf incompatible with recommended bcftools (v1.19).0 votes 7 comments
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depth of coverage total summary should not be 100.0 Answered0 votes 7 comments
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Issue with combining g.vcf files Answered0 votes 7 comments
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how to combine mutect2 and haplotypecaller vcfs from the same sample Answered0 votes 7 comments