Can't decompress Genome STRiP tar.gz file normally
I downloaded both the latest versions of 2016 and 2017; both failed to be decompressed with `tar xzf svtoolkit_*.tar.gz' on Ubuntu 16.04 and 14.04: tar: This does not look like a tar archive tar:...
View ArticleTransloation detection on sex chromosome with one batch data?
We have a batch of data from 8 subjects generated with Ion Proton sequencer. We are interested in detecting translocation events in these subjects. We do not have reference data from other subjects....
View ArticleA Variant which is supported by 21 reads in IGV is not called by...
Below command is used for the purpose java -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fa -I 62352575_S28_realigned.bam -L nexterarapidcapture_exome_target_region.bed...
View ArticleInstalling GATK through cygwin
Hi ya'll I don't have access to the specific instructions for installing GATK on a windows platform (i.e. using cygwin). If I could get permission or someone could walk me through this I would be...
View ArticleClik here to view.
Malformed walker argument
Hello, I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message: java -jar GenomeAnalysisTK.jar -T IndelRealigner...
View ArticleCan mutect2 be used for sequence data from pooled-Seq?
Hi, I am using Haplotype caller to call variants from WGS samples on pooled individuals. I wonder if there is a benefit to using Mutect2 in this case? Is it better controlling for ploidy effects...
View ArticleIs it possible to suppress the NON_REF tag on variant calls?
Hello, In GVCF output from HaplotypeCaller, each line contains the allele, including the lines with explicit variant calls. Is there a simple way to suppress the allele on variant calls? Also, what is...
View ArticleFindCoveredIntervals -minBQ -minMQ -cov
Hello Admin's, When running FindCoveredIntervals for GATK version 3.3-0: java -Xmx20g -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R Homo_sapiens_assembly19.fasta -I s_C_000036_T001_d.bam -minBQ...
View ArticleAbnormal genome plot running GATK4 CNV workflow
Hi GATK team, I am a new user of GATK4 CNV workflow. I can get all the output files from computing steps. They all look fine. However, the read dots are missing in the resulting PNG files. I can only...
View ArticleVersion highlights for GATK version 3.5
The last GATK 3.x release of the year 2015 has arrived! The major feature in GATK 3.5 is the eagerly awaited MuTect2 (beta version), which brings somatic SNP and Indel calling to GATK. This is just the...
View ArticleClik here to view.
Should I analyze my samples alone or together?
Together is (almost always) better than alone We recommend performing variant discovery in a way that enables joint analysis of multiple samples, as laid out in our Best Practices workflow. That...
View ArticleMutSigCV -- too few driver genes
using WES data from 85 patients, I get only 1 significant (5%) driver mutation gene. We are working on melanoma data, so mutation rate is very high, I know. But is there any parameter I can adjust to...
View ArticleVQSR error: NaN LOD value assigned
INFO 17:05:50,124 GenomeAnalysisEngine - Preparing for traversal INFO 17:05:50,144 GenomeAnalysisEngine - Done preparing for traversal INFO 17:05:50,144 ProgressMeter - [INITIALIZATION COMPLETE;...
View ArticleMoved: Oncotator reports on error, could you please help?
This discussion has been moved.
View ArticleWhat's the difference between b37 and hg19 resources?
Hi, all. I have questions on resource bundles. Are the 'hg19' bundle files just liftover from 'b37' bundles in UCSC-style? If so, why are there some variants in only one version and not the other? For...
View ArticleSelectVariants According to AD Values
How can I select variants that has specific AD values? Since AD parameter has two values (reference depth, allele depth) I couln't find that how can I write related expression on script. If I wanted to...
View ArticleDP question
Hi there, Can somebody please confirm why DP in Info and Format fields are different. My assumption is Info field DP (847 in example below ) includes reads that failed Haplotype Caller filter......
View ArticleClik here to view.
LeftAlignAndTrimVariants --splitMultiallelics changes GT from known to unknown
I have a VCF file with this line (i.e. GT=0/1=G/T): 20 10120854 . G T,A 32175.56 . AC=399,18;AF=0.111,5.006e-03;AN=3596;BaseQRankSum=1...
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 ArticleHow can I annotate with dbsnp and also include info fields from dbsnp vcf?
I want to annotate my vcf using dbsnp, however I don't want to add only the dbsnp rs#s in the ID field. I also want to add INFO fields from the dbsnp vcf into the annotated vcf. How can this be...
View Article