Results GATK v2.7 vs. v3.7
Dear GATK team, I have started to re-analyse some samples, which I had analysed a long time ago with v2.7 - mainly because a new reference genome has become available for this organism. The old...
View ArticleOutputting REF calls in Mutect
Hi. I wonder if there's any way to output REF calls with MuTect, so that I can distinguish them from no-calls? What I'd like to obtain is a confidence-score for ref calls, i.e. GT:PL 0/0:0,255,255...
View ArticleHow does the BwaSpark in GATK4 control the number of threads?
I tried to ERR000589 process data with BwaSpark. The bam file size is 1.3G. The average time spent is about 25 min (5 nodes). However it would only cost 5 min in processing same data if I tried to use...
View ArticleERROR MESSAGE: Unable to read index file, for input source
ERROR MESSAGE: Unable to read index file, for input source:xxx.g.vcf.idx hi, GATK team. I have 235 human exome sequencing samples. I use the haplotype caller in gvcf mode and generate g.vcf per sample....
View ArticleVariantRecalibration needs -mG 4 with per lane fastq, but not concatenated...
The headline is a bit imprecise because of the length limit, so what I mean to say is that when I run a NA12878 sample through my pipeline with the fastq files split per lane, I need to use -mG 4 in...
View ArticleERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the...
Hi, I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file. C1_lenght=155648...
View ArticleGATK didn't Output the InDel I expected
Hi! I used GATK to call InDel and SNP with my sequence data. But GATK didn't give any output variations(InDel and SNP). So, I use GATK to generate a "bamout file" showing how HaplotypeCaller has...
View ArticleRemoval of Phone Home
Hi, I've been reading about the removal of the Phone Home option from GATK versions 3.6 and on. It wasn't entirely clear to me whether the whole reporting system was taken out from the code or just the...
View ArticleWorkflow for artificial reporter amplicon analysis
Hello, We are working on a project of sequencing of an artificial reporter from human cell line using miSeq (2x300bp). We used PCR method to obtain the amplicons (with UMIs). We are currently stuck at...
View ArticleCombineVariants 'set' value separator is dash but can it be changed
I have a request for CombineVariants: can the separator between values in the "set=" keyword that is added to the INFO column be settable to something other than "-" (which I use in my sample names)?...
View ArticleHow to fix this error message?
ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version exported): ERROR ERROR This means that one or more arguments or...
View ArticleHow to handle consecutive indels?
Hi all, I have one question regarding indels in vcf. Here is an example of consecutive indels from vcf file. chr pos ref alt chr1 218616012 TTC T,* chr1 218616013 TC T,* I believe, these two indels are...
View ArticleWhat's the version of bwa being implemented in GATK4 bwaspark tool?
Hi, Is the bwa of the bwaspark tool is the latest 0.7.15 version or not? Thanks!
View ArticleWhat version of bwa is being used by the BwaSpark tool?
Another person asked this same question here http://gatkforums.broadinstitute.org/gatk/discussion/8308/whats-the-version-of-bwa-being-implemented-in-gatk4-bwaspark-tool, but it was never answered....
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 ArticleMissing gentoypes despite high number of reads
Dear GATK-team GenotypeGVCFs, sets all genotypes as missing for a large part of a gene I am interested in, even though there seem to be lots of reads in all individuals for those sites. I have the same...
View Articlemin base quality and min mapping quality and -rf flag
Hi I wan to apply two filters for the haplotype caller in the GVCF mode. These are min base quality and min mapping quality. -mbq 20 -mmq 30 But I am not sure about to specify the read filter flag like...
View ArticleCanFam3.1 variation files, convert to vcf?
I have resequencing data from a case-control study that I am trying to analyse. I have mapped my reads using bwa, applied FixMateInformation (.jar picard), added metadata (AddOrReplaceReadgroup.jar)...
View ArticleVariantFiltration - FORMAT Required
Hi, Dear GATK Community, I am running VariantFiltration on my VCF file that has no FORMAT and SAMPLE column and it gives me the following error: ERROR MESSAGE: Your input file has a malformed header:...
View ArticleI can't download the bundle2.8(hg37) because connection to the server is...
Hi, Broad Institute Members. I'm trying to download bundle2.8 of hg37 from the public FTP server. But I can't access the server (connection is refused). What do I need to do to get the bundle? echo...
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