SelectVariants error
I`m calling SNP by haplotype caller,and i got vcf document for each sample. After that , i use selectvariant to select variants of SNP . But i got this error: ERROR...
View Articlehow to filter mutation pattern
Hi GATK team. Now, I want to filter out known variants from VCF file. I have annotated VCF file with dbsnp146, and I would like to filter with mutation patterns of dbsnp, but not rsIDs. So, I have been...
View ArticleSelectVariants hangs while filtering out the biallelic SNP's
System specification The version of my JAVA is: 1.7.0_79 The version of my GATK is: 3.7.0 My OS is: Ubuntu 14.04.2 LTS My processor is: Intel Core i5-4440 CPU @ 3.10GHz × 4 I have been successful in...
View Articlewho may have stood a return constructing 18 stadiums
Leiweke, who may have stood a return constructing 18 stadiums and also circles round the region, found the actual attractiveness. The area, just upper from the Ybor Channel and also Selmon Expressway,...
View ArticleNeed Bluetooth Beacon for Marketing and Advertising?
I currently want to use proximity Iotton beacons for marketing and advertising. How far does this reach? Once configured, will I be able to broadcast custom message?
View ArticleGermline Pipeline - Codon invalid error
I am struggling with the Germline Pipeline available from the Algorithm_Commons workspace on Firehose. All of the samples I am trying to process with this workflow were sequenced at the Broad, either...
View ArticleWhere is the dbSNP information in oncotator result maf?
Hi! I use oncotator v1.9 to annotate Tumor-Normal paired somatic variants in MAFLITE format. As the document described, there are 26 datasources: _Oncotator v1.9.0.0 | Flat File Reference hg19 |...
View ArticleERROR stack trace: Somehow the requested coordinate is not covered by the...
when I use MuTect2 -nct * for calling step(version 3.6 and allso in 3.7 version), I got this error: ERROR stack trace org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the...
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Metrics say percent – Double-check those decimals – Fractions everywhere
Picard metrics that say 'percent' actually mean 'fraction'. Let's take metrics from MarkDuplicates as an example. Under PERCENT_DUPLICATION we see 0.134008. If we divide READ_PAIR_DUPLICATES by...
View ArticleRunning standalone Mutect and getting error..!! How can I resolve it?
I want to run Mutect on my data. I have bam files of normal control and tumor data. I used the dbsnp and cosmic files given in the Mutect documentation. Reference human genome is hg19. I get the...
View ArticleHow to prepare interval list for " " argument while running Mutect?
I am not sure how to prepare the interval list for my data to pass as "intervals" argument while running Mutect?
View ArticleGATK 3.8 log4j error
I just upgraded from GATK 3.7 to the newly released GATK 3.8 (3.8-0-ge9d806836) and I am getting a StatusLogger error: ERROR StatusLogger Unable to create class...
View Article(HOWTO) Run GATK CNV (and GATK ACNV) using premade Queue scripts (Broad...
Notice: these workflows are out of date and should no longer be used. See the WDL scripts instead. These workflows are not officially supported, but are used extensively, internally, for our...
View ArticleMuTect2: ERROR MESSAGE: Somehow the requested coordinate is not covered by...
Hi guys, I use mutct2 to do somatic variant calls, and got this ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions? I searched the forum and found people got...
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I need to run programs that require different versions of Java
We sometimes need to be able to use multiple versions of Java on the same computer to run command-line tools that have different version requirements. At the time of writing, GATK requires an older...
View ArticleGATK4.beta6 GenomicsDBimport error
I've been trying to run GenomicsDBimport on 2000+ samples. It worked on GATK4.beta3, but there was an error in the batch processing so I switched to beta6. In this version, I'm getting an error with...
View ArticlePE mates are lost while downsampling with -dfrac?
Hi GATK team and users, I am using PrintReads with -dfrac option to simulate different depths of coverage. The original data contains WGS, PE reads (from GATK's Bundle bam, PrintReads with -L 20,...
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...
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Scaling up joint calling with GenomicsDB
What's new in GATK4? In this short video, Laura Gauthier explains how the speed and scalability of joint calling is dramatically improved in GATK4 thanks to the Intel GenomicsDB datastore.
View Articlelower quality score after BQSR
Happy new year! I am doing BQSR in a non-model organism. So I did a first round of BQSR, and extract the highest 20%SNPs according the quality score ("QUAL"column) to use as a known dbSNP dataset. But...
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