Forum Login Issue:
Currently the "Log in with Google" button redirects you to a "Page not found." This is an issue that our forum vendors are working on fixing. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
ex: https://gatkforums.broadinstitute.org/gatk/gatk/entry/...
Currently the "Log in with Google" button redirects you to a "Page not found." This is an issue that our forum vendors are working on fixing. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
ex: https://gatkforums.broadinstitute.org/gatk/gatk/entry/...
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RE: How to best minimize variation between runs of HaplotypeCaller in GVCF mode?
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ANN1002 -
Question about ASEReadCounter
Dear GATK team, -
RE: [GATK4 beta] no filter-passing variants in Mutect2 tumor-only runs using default parameters
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 -
RE: Off-label workflow to simply call differences in two samples
newline="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" -
RE: How to force MuTect2 genotype all sites within intervals?
Hi Sheila, -
Mutect2 GATK 3.8 strange report
#CHROM POS ID REF ALT QUAL FILTER INFO F -
RE: Best strategy to "fix" the Haplotype Caller - GenotypeGVCF "missing DP field" bug??
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_01 -
GenotypeGVCFs output is empty gvcf file
I ran java -Xmx48g -jar gatk/3.5-0/src/GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19/hg19.fa -V merged.240samples.chr22.gvcf.gz -o merged.jointGT.chr22.gvcf.gz -
Exception Running CombineGVCFs
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 2686_DSTL_8 -
RE: HaplotypeCaller warnings DepthPerSampleHC
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 3894STDY7081741 3894STDY7081742 3894STDY7081743 3894STDY7081744 3894STDY7081745 3894STDY7191358