New User Advice
Show all
Sort by newest post
-
Script for using same GATK tool(s) on multiple sample files0 votes 0 comments
-
Creating dictionary for fasta reeference file0 votes 0 comments
-
Combining mplileup and haplotypeCaller calls Answered0 votes 2 comments
-
Help with WDL workflow for mutec2?0 votes 5 comments
-
looking for panel of normals and allele frequency for hg19 genome build Answered0 votes 1 comment
-
picard CollectAlignmentSummaryMetrics required arguments format Answered0 votes 1 comment
-
gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) Answered0 votes 3 comments
-
ValiidateSamFile Error: Mate not found Answered0 votes 9 comments
-
Mutect2 with and without UMI information Answered0 votes 1 comment
-
7 things I learned while reprocessing my WGS data on Terra: part 10 votes 1 comment
-
Picard CheckIlluminaDirectory - Issue with file/folder structure?0 votes 1 comment
-
VQSR dataset preparation Answered0 votes 2 comments
-
Updating Picard to latest version Answered0 votes 1 comment
-
Distinct allele frequency patters by HaplotypeCaller and Mutect2 for the same sample Answered0 votes 1 comment
-
Running best practices workflow step-by-step in command line1 vote 1 comment
-
Why doesn't haplotypecaller use PON?0 votes 1 comment
-
Failed on the variants calling with low quality pacbio seq Answered0 votes 1 comment
-
Invalid or corrupt jar file Answered0 votes 3 comments
-
DP for each variant bulk is skewed towards 50 and multiples of 500 votes 7 comments
-
How do I pool normal samples in mutect2? Answered0 votes 1 comment
-
Problems with FastQtoSAM0 votes 3 comments
-
At which stage family genotype posterior recommened in germline discovery best practice? Answered0 votes 1 comment
-
Counld I use bam files from HISAT2 to call snp/indels?0 votes 2 comments
-
Somatic Structure Variation on exome-seq data0 votes 1 comment
-
Sensitive Copy Ratio Pipeline compatibility with tool "mergeLevels"0 votes 1 comment
-
Scatter / Gather for BaseRecalibrator on a single human WES dataset0 votes 2 comments