Picard CheckIlluminaDirectory Failing
Hello, I have a MiSeq run that I wish to run ExtractIlluminaBarcodes and IlluminaBasecallsToSam on, however, they can't find the files needed. When I run CheckIlluminaDiretcory I get this result...
View ArticleUsing JEXL to apply hard filters or select variants based on annotation values
1. JEXL in a nutshell JEXL stands for Java EXpression Language. It's not a part of the GATK as such; it's a software library that can be used by Java-based programs like the GATK. It can be used for...
View ArticleMNP calling problem in GATK4 Mutect2 beta
Hi, I tried to use GATK4 Mutect2 to call somatic mutations and found some weird MNP results: CHROM POS REF ALT chr2 157214886 GT TT chr4 130772884 CGTGT TGTGT chr4 145617203 TAAA AAAA chr5 7857891 CAA...
View ArticleSave the date: online event January 9 for the GATK 4.0 release
To celebrate the release of GATK 4.0, a project more than two years in the making, we're planning a Facebook Live event during which we'll livestream a series of presentations and discussion panels....
View Article" MESSAGE: I/O Error while reading input-output map file "
Hi, Using: 1. jdk1.8.0_131 for java 2. GATK version 3.8-0-ge9d806836 3. csh I got this error which I cannot understand, I don't know what an input-output file is... Here is the complete output of the...
View ArticleHow to get the idetail of regions getting fixed during Split'N'Trim step
I am following GATK procedure given at https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq . After doing all step wise analysis, I am curious to check regions getting...
View ArticleHaplotypeCaller/ Variantannotator no allele balance tag for all SNPs
Version 3.1.1. Human normal samples. I couldnt find AlleleBalance and AlleleBalanceBySample tags in my vcf outputs. Tags are not found even for single variant I tried HaplotypeCaller with -all or...
View ArticleClik here to view.
Deep learning in GATK4
By Sam Friedman, deep learning developer in GATK4 Over the past couple of weeks, there's been a lot of chatter online --and in the press!-- about the applicability of deep learning to variant calling....
View Articlepicard FilterSamReads : "samtools sort -n" is not solve my problem
Hi, I used follow command to filter my sorted bam file: java -jar picard.jar FilterSamReads I=input.bam O=out.bam READ_LIST_FILE=read_names.txt FILTER=excludeAligned But the error just as below: [Fri...
View ArticleComparison of FreeBayes and GATK info fields
Hello, I am trying to compare two VCFs: one generated by FreeBayes (multi-sample) and one by GATK (multi-sample generated by Genotype GVCFs). Before I compare the two I need to filter both, and I'm...
View ArticleMutect2 parallel problem
Dear GATK team. I am using Mutect2 to call somatic mutation from tumor/normal paired sample. However after jobs running for 8 days, our server has been rebooted for some reason. Most of the jobs are...
View ArticleSAM/BAM/CRAM file malformed
Hi, I get this error while running BaseRecalibrator : Command : java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R ucsc.hg19.fasta -I P003_F1_S2_dedup_reads_RG.bam -knownSites:dbsnp,VCF...
View ArticleInconsistency between Alt Variant in BAM and bamout from MuTect2
I have a BAM from MarkDuplicates, Realigned and Recalibrated pipeline showing only 2 reads with deletion. After MuTect2 pipeline the somatic genotype shows 6 reads (marked below). I have only found 2...
View ArticleMUTECT helo interpreted it
Dear, I have executed the mutect and I am not understand the result. In the example below. The variants are present in COSMIC, but were REJECT by the MUTECT filter. Could you explain the reason??...
View ArticlePrintReads gets stuck
Hi GATK team! I am trying to do somatic variant calling with RNAseq data (following GATK best practices with paired-end Illumina reads). I have normals and tumors, and my pipeline runs from the fastq...
View ArticleGet free credits worth $250 for running GATK4 pipelines in the cloud!
With the GATK4 release just around the corner, we wanted to make it easy for everyone to try out the new pipelines without going through a whole lot of setup. So we're setting them all up in...
View ArticleGATK and MuTect licensing moves to direct-through-Broad model
We have some important news to share with you regarding the licensing of GATK and MuTect. The licensing agreement between us and Appistry will end effective April 15, 2015; from that point on, the...
View ArticleHow to now if a Combined vcf file is calibrated with GATK or not
Dear GATK using community Pardon me for my ignorance, but I am new with using NGS pipelines. I have recieved a combined VCF file or 200 samples. The only information I was able to understand from VCF...
View ArticleWhat's the meaning of "population" option in ContEst
I wanna use ContEst to estimate contamination for mutect2. I am confused by "--population" option. I don't understand the meaning of "evaulate contamination for just a single contamination population"....
View Article