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20
289
Views

base recalibrator --known-sites argument does not work

Published on
#java #windows-subsystem-for-linux #ubuntu-20.04 #vcf-variant-call-format #gatk
303
Views

Parsing FORMAT and sample value fields from VCF file

Published on
#r #tidyverse #tidyr #vcf-vcard #gatk
58
Views

Troubleshooting GATK Pipeline Error in AWS ParallelCluster Environment and Spark

Published on
#amazon-web-services #apache-spark #gatk
92
Views

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

Published on
#python #bioinformatics #snakemake #gatk
207
Views

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

Published on
#python #snakemake #gatk
139
Views

What does 'NEGATIVE_TRAIN_SITE' in VQSR mean?

Published on
#vcf-variant-call-format #gatk
49
Views

GATK Variant Filtration file Anopheles gambiae s.s

Published on
#filtering #variant #gatk
102
Views

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

Published on
#maven #java-8 #gatk
1.1k
Views

gatk VariantRecalibrator positional argument error

Published on
#gatk
1.4k
Views

Combine a directory of GVCF files with gatk CombineGVCFs

Published on
#gatk
853
Views

Getting GATK argument error and dont understand?

Published on
#bash #alignment #sequence #dna-sequence #gatk
460
Views

MuTect install: GATK-protected: maven: Java-compile-error

Published on
#java #maven-3 #gatk
2.7k
Views

Running docker from bash script

Published on
#bash #docker #gatk
194
Views

Snakemake: create multiple wildcards for the same argument

Published on
#linux #wildcard #snakemake #gatk
2k
Views

How to run ensembl-vep in conda

Published on
#variant #vcf-variant-call-format #vcftools #gatk
329
Views

Error running gatk HaplotypeCaller with allele specific annotations

Published on
#variant #gatk
56
Views

Snakemake first genotype of a vcf file as wildcard in output

Published on
#python #snakemake #gatk
562
Views

Snakemake integrate the multiple command lines in a rule

Published on
#python #bash #shell #snakemake #gatk
578
Views

GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

Published on
#java #multithreading #gatk
27
Views

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

Published on
#java #r #ubuntu #variant #gatk

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