StackOverflow Questions for Tag: gatk

Wei-Chen Pan

Reputation: 3

User Error after running GATK BaseRecalibrator for WGS BAM file

snakemakegatk

Score: 0

Answers: 0

Franz

Reputation: 35

How to deal with paired tumor-normal samples in Snakemake?

pipelinesnakemakebamgatk

Score: 0

Answers: 1

Wei-Chen Pan

Reputation: 3

Error when Running Picard or GATK MergeVcfs Using Snakemake

mergesnakemakegatkpicard

Score: 0

Answers: 1

agre945

Reputation: 1

GATK jar file not found- Using GATK on an HPC

condahpcgatk

Score: 0

Answers: 0

user22752471

Reputation: 3

I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process

javarubuntuvariantgatk

Score: 0

Answers: 0

milcs40

Reputation: 5

Parsing FORMAT and sample value fields from VCF file

rtidyversetidyrvcf-vcardgatk

Score: 0

Answers: 1

user22752471

Reputation: 3

base recalibrator --known-sites argument does not work

javawindows-subsystem-for-linuxubuntu-20.04vcf-variant-call-formatgatk

Score: 0

Answers: 1

Mike

Reputation: 1161

gatk VariantRecalibrator positional argument error

gatk

Score: 0

Answers: 1

Cora_olpe

Reputation: 43

GATK4 is rejecting my RGSM when using AddOrReplaceReadgroups

gatk

Score: 0

Answers: 1

Greg Dougherty

Reputation: 3471

New: Fatal error compiling: java.lang.NoClassDefFoundError: com/sun/tools/javac/main/OptionName: com.sun.tools.javac.main.OptionName

mavenjava-8gatk

Score: 0

Answers: 0

dthorbur

Reputation: 1091

GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

javamultithreadinggatk

Score: 2

Answers: 2

Ari Miller

Reputation: 1

How do I use this python function within the params section of my Snakemake rule?

pythonbioinformaticssnakemakegatk

Score: 0

Answers: 0

Mike

Reputation: 1161

Error running gatk HaplotypeCaller with allele specific annotations

variantgatk

Score: 0

Answers: 1

user3224522

Reputation: 1151

Snakemake integrate the multiple command lines in a rule

pythonbashshellsnakemakegatk

Score: 3

Answers: 3

user3224522

Reputation: 1151

Snakemake first genotype of a vcf file as wildcard in output

pythonsnakemakegatk

Score: 0

Answers: 1

Mike

Reputation: 1161

How to run ensembl-vep in conda

variantvcf-variant-call-formatvcftoolsgatk

Score: 2

Answers: 1

Mike

Reputation: 1161

Combine a directory of GVCF files with gatk CombineGVCFs

gatk

Score: 2

Answers: 1

user3224522

Reputation: 1151

Snakemake: create multiple wildcards for the same argument

linuxwildcardsnakemakegatk

Score: 0

Answers: 1

JEJI

Reputation: 59

What does 'NEGATIVE_TRAIN_SITE' in VQSR mean?

vcf-variant-call-formatgatk

Score: 1

Answers: 0

Shafayet Rahat

Reputation: 253

snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

pythonsnakemakegatk

Score: 2

Answers: 1

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StackOverflow Questions for Tag: gatk

User Error after running GATK BaseRecalibrator for WGS BAM file

How to deal with paired tumor-normal samples in Snakemake?

Error when Running Picard or GATK MergeVcfs Using Snakemake

GATK jar file not found- Using GATK on an HPC

I dont get the output file to &quot;gatk CollectAlignmentSummaryMetrics&quot; that use to get alignment and insert size metrics in variant calling process

Parsing FORMAT and sample value fields from VCF file

base recalibrator --known-sites argument does not work

gatk VariantRecalibrator positional argument error

GATK4 is rejecting my RGSM when using AddOrReplaceReadgroups

New: Fatal error compiling: java.lang.NoClassDefFoundError: com/sun/tools/javac/main/OptionName: com.sun.tools.javac.main.OptionName

GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

How do I use this python function within the params section of my Snakemake rule?

Error running gatk HaplotypeCaller with allele specific annotations

Snakemake integrate the multiple command lines in a rule

Snakemake first genotype of a vcf file as wildcard in output

How to run ensembl-vep in conda

Combine a directory of GVCF files with gatk CombineGVCFs

Snakemake: create multiple wildcards for the same argument

What does &#39;NEGATIVE_TRAIN_SITE&#39; in VQSR mean?

snakemake multiple parameters for multiple input and single output in snakemake. ConbineGVCFs gatk problem

I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process

What does 'NEGATIVE_TRAIN_SITE' in VQSR mean?