Special GATK Use Cases
Information here covers items that are not in Best Practices but may someday be a part of Best Practices
-
Using Mutect2 on Mac M11 vote 0 comments
-
How do I know why gatk is removing some of my reads for geotyping?0 votes 0 comments
-
java.lang.NullPointerException error in VariantQC0 votes 3 comments
-
DepthOfCoverage gives ~100% coverage for ultra-deep sequencing data0 votes 3 comments
-
VariantsToTable cannot deal with deletion correctly0 votes 2 comments
-
variant calling with allotetraploid species0 votes 1 comment
-
HaplotypeCaller does not work Answered0 votes 2 comments
-
use_jdk_deflater not defined?0 votes 1 comment
-
Using gatk VariantFiltration to filter ONT wf-artic generated VCF files0 votes 5 comments
-
Read Group (UNKNOWN) is not a recognized platform1 vote 1 comment
-
CombineGVCFs - elements of input iterator not sorted Answered0 votes 2 comments
-
gatk CombineGVCFs Answered0 votes 2 comments
-
BaseRecaliberator .fai file error0 votes 1 comment
-
RAD-seq Variant calling0 votes 1 comment
-
GATK error Answered0 votes 4 comments
-
GATK HaplotypeCaller issues with Genotyping (GT)0 votes 3 comments
-
HaplotypeCaller output not generated, no error Answered0 votes 1 comment
-
DepthOfCoverage Output Files Empty - mtDNA0 votes 1 comment
-
incomplete output when running ASEReadCounter Answered0 votes 5 comments
-
Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites? Answered0 votes 6 comments
-
Monomorphic sites after GenotypeGVCFs --include-non-variant-sites Answered0 votes 8 comments
-
HaplotypeCaller not writing output Answered0 votes 1 comment
-
--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' Answered0 votes 1 comment
-
Standalone HaplotypeCaller Answered0 votes 5 comments
-
Genotype concordance - dictionaries are not the same size Answered0 votes 1 comment
-
java.lang.ArrayIndexOutOfBoundsException: 32770 while using GenotypeGVCFs Answered0 votes 1 comment
-
Find variants with HaplotypeCaller on MAPQ0 regions0 votes 1 comment
-
no read counts per allele while using gatk ASEReadCounter Answered0 votes 11 comments