Special GATK Use Cases
Information here covers items that are not in Best Practices but may someday be a part of Best Practices
Show all
Sort by votes
-
After apply gatk ApplyBQSR, the total reads become less1 vote 2 comments
-
Mutect2 Somatic-vs-Somatic calling1 vote 6 comments
-
Picard CrosscheckFingerprints with multi-sample VCF1 vote 5 comments
-
ASEReadCounter - What to use as the VCF variant reference1 vote 1 comment
-
does GATK offers to match alleles in two vcf files?1 vote 1 comment
-
gatk pileup result lost some reads cover?1 vote 2 comments
-
Using Mutect2 on Mac M11 vote 1 comment
-
How do I know why gatk is removing some of my reads for geotyping?1 vote 0 comments
-
Read Group (UNKNOWN) is not a recognized platform1 vote 1 comment
-
Maximum performance HaplotypeCaller Answered1 vote 10 comments
-
Mutect for Somatic SNVs in Highly Polymorphic Genome Regions Answered1 vote 3 comments
-
Common germline variants sites VCF for GetpileupSummaries for mouse data Answered1 vote 7 comments
-
has sample entries that don't match the other files. Answered1 vote 1 comment
-
Generating COSMIC.db Data Source for Funcotator0 votes 0 comments
-
DetermineGermlineContigPloidy generating error0 votes 2 comments
-
Mutect2 Calls for non-tumor pooled samples - no variants pass filters0 votes 7 comments
-
snp calling using a reference VCF file to define all interesting position0 votes 5 comments
-
GATK-VQSR issue0 votes 12 comments
-
gatk baserecalibrator no error reported, but no output generated0 votes 6 comments
-
Mutect2 calls germline variants not present in germline resource0 votes 4 comments
-
1001_Genome project0 votes 1 comment
-
CombineGVCFs produces .bcf incompatible with recommended bcftools (v1.19).0 votes 7 comments
-
CreateSomaticPanelOfNormals (BETA) workflow0 votes 1 comment
-
haplotypecaller: possible to generate phased vcf from phased bam?0 votes 1 comment
-
GenomicsDBImport Memory and Disks0 votes 1 comment