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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genomicsdbimport add new samples0 votes 1 comment
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PathSeqPipelineSpark: Failed to map segment from shared object ERROR0 votes 2 comments
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GATK concordance0 votes 5 comments
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issue while running mitochondrial analysis0 votes 8 comments
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Aligning very short reads0 votes 1 comment
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depth of coverage total summary should not be 100.00 votes 1 comment
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picard.PicardException: Start on sequence 'chr1' was past the end: 565891 < 627380 Answered0 votes 1 comment
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HaplotypeCaller does not recognize alternative placement of an indel in a repetitive region Answered0 votes 5 comments
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GVCF vs VCF INFO tags, relevance for filtering RNAseq SNPs0 votes 2 comments
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Genotype several gvcf files at only few thousands positions Answered0 votes 1 comment
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Picard "Too many open files" Answered0 votes 2 comments
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Maximum performance HaplotypeCaller0 votes 3 comments
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Running GATK for detecting translocations in targeted single-cell DNA-seq Answered0 votes 3 comments
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GATK-SV GenotypeBatch: svtk count error0 votes 3 comments
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Trouble using GATK: gVCF files missing the <NON_REF> tag Answered0 votes 1 comment
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GenotypeGVCFs -all-sites Answered0 votes 1 comment
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Error using CombineGVCFs - Exception thrown at Chr0 votes 6 comments
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Get a multi-sample GVCF file from genomicDB? Answered0 votes 1 comment
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how can I create an interval list for spark analysis of a non-human genome Answered0 votes 1 comment
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combine GVCF Answered0 votes 2 comments
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GVCF0 votes 1 comment
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Some working examples of SelectVariants and JEXL queries. Completed0 votes 1 comment
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functactor Answered0 votes 4 comments
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reads filtered by Mutect2 having MAPQ 25 Answered0 votes 8 comments
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HaplotypeCaller --max-reads-per-alignment-start Answered0 votes 1 comment
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Issue with combining g.vcf files Answered0 votes 7 comments
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CombineGVCFs Answered0 votes 5 comments
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running haplotypecaller on bam files with csi indexed format instead of bai Answered0 votes 1 comment
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java.lang.OutOfMemoryError using BaseRecalibrator Answered0 votes 3 comments