BCL to uBAM tutorial update
Hi there, I'm very interested on try the BCL to uBAM protocol (Tutorial#6570 coming soon) you have mentioned on your article #6483 ((How to) Map and clean up short read sequence data efficiently). Do...
View ArticleIs Panel of Normals compatible between MuTect1 and MuTect2?
Is Panel of Normals compatible between MuTect1 and MuTect2? I wonder if PoN created from either tool can be used for the other. Thanks!
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Support team appreciation day -- say hi and get a prize
I want to give mad props to my team. Every day they handle new questions about obscure error messages or unusual experimental designs, on top of their ongoing efforts to develop new documentation...
View ArticleD-ToxoG input
Some paper use D-ToxoG to filter oxog artifacts after running** Mutect1** (not Mutect2) . But D-ToxoG input needs some specific columns that common MAF or VCF file didn't provide. For example,...
View ArticleUnifiedGenotyper in GATK4?
Hi, Are there plans to include UnifiedGenotyper in GATK4? I know the focus is now on development of HaplotypeCaller, but UnifiedGenotyper is has features that make it work better in targeted...
View ArticleQuestion: Question: Mutect 2 and related vcf in GDC
There are 2 vcf files from the DNA sequencing available in GDC: one for the tumor and the other one for the normal sample. I'm a little confused about the presence of the normal vcf file. Is this file...
View ArticleHadoop error?
Hello, I am trying to run GATK 4 on a cluster with human data (NA12878) but it seems there is a problem (maybe with hadoop install as the warning says?). Below is the command line and error. Thanks for...
View ArticleDP is missing from the Mutect2 GATK 4 beta
Dear Developers, I called the variants with Mutect2, GATK4 (beta). Reading the file header, I see that it suppese to have AD and DP FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths...
View Article#CHROM characters allowed
Hello, I am trying to use GENOTYPE_GIVEN_ALLELES through HaplotypeCaller and have never run into this problem before. Everything is running as I expect, however I am really not getting any results even...
View ArticleGATK4.alpha emitDroppedReads option
Does GATK4.alpha support -emitDroppedReads option that works with -bamout?
View ArticleRegarding Whole genome CNV calling best practices
Dear GATK team, I am looking best practices for calling germ-line Whole genome copy number variations. I have seen such option at best practices page on GATK...
View ArticleCalculateGenotypePosteriors ArrayIndex Out of Bounds Error - Using v3.6
Hi I get the following ArrayIndexOutOfBounds Error while running CalculatingGenotypePosteriors for GiaB ChineseTrio samples. I have repeated the run three time and the error is reproducible every time....
View Articlewhat's mean realn?
hi First of all, I am poor at English so it will be inconvenient to read.I'm sorry. I'm studing a script. /usr/local/SAMtool/1.3.1/samtools flagstat...
View ArticleConvert bams to vcf files
Hi, I have bam files downloaded from the 1000 Genomes Project and I need to have fasta files as the reference files (for -R option) in order to turn my bams into vcf files. Can you please tell me where...
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(How to) Map and clean up short read sequence data efficiently
If you are interested in emulating the methods used by the Broad Genomics Platform to pre-process your short read sequencing data, you have landed on the right page. The parsimonious operating...
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(How to) Call somatic copy number variants using GATK4 CNV
Presented tools are in BETA. Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section....
View ArticleUnknown genotypes with large support
We have a set of 20 fungi sequenced (Illumina NextSeq 150x2) at high coverage we are analyzing for SNPs. After the GATK (First with 3.4, later at 3.7) analysis, filtering, and removing our 'fixed' snps...
View ArticleWeb-based Oncotator server
There is a web-based version of Oncotator which you can use for annotation without running anything on your own machine. However, please note that the web-based version is an older version, with fewer...
View ArticleVariant recalibration in GATK4 alpha
Are the VariantRecalibrator and ApplyRecalibration tools available in GATK4 alpha? I'm unable to locate them or anything that looks like them in the list of tools
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