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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Generating COSMIC.db Data Source for Funcotator0 votes 0 comments
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Mutect2 Calls for non-tumor pooled samples - no variants pass filters0 votes 7 comments
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DetermineGermlineContigPloidy generating error0 votes 2 comments
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snp calling using a reference VCF file to define all interesting position0 votes 5 comments
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GATK-VQSR issue0 votes 12 comments
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gatk baserecalibrator no error reported, but no output generated0 votes 6 comments
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Maximum performance HaplotypeCaller Answered1 vote 10 comments
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GetPileupSummaries Error: java.lang.OutOfMemoryError: Java heap space Answered0 votes 11 comments
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Mutect2 calls germline variants not present in germline resource0 votes 4 comments
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Mutect2 - using a primary tumour sample instead of a normal sample0 votes 3 comments
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CombineGVCFs produces .bcf incompatible with recommended bcftools (v1.19).0 votes 7 comments
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1001_Genome project0 votes 1 comment
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CreateSomaticPanelOfNormals (BETA) workflow0 votes 1 comment
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haplotypecaller: possible to generate phased vcf from phased bam?0 votes 1 comment
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GenomicsDBImport Memory and Disks0 votes 1 comment
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SelectVariants discordance gives no discordance0 votes 4 comments
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PathSeq error: java.lang.NumberFormatException0 votes 8 comments
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GenotypeGVCFs0 votes 3 comments
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RFE Picard CollectWgsMetrics: allow reporting coverage between 0 and 1X0 votes 1 comment
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After apply gatk ApplyBQSR, the total reads become less1 vote 2 comments
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Force-calling mode in Mutect20 votes 3 comments
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"force calling" mode in HaplotypeCaller0 votes 1 comment