Error while running HC on ChrX
Dear GATK, I have a set of 4 bam files that I was able to generate genotypes from using HaplotypeCaller for Chr20. I took the same data and tried to call genotypes for ChrX, and received the following...
View ArticleError when I called variants using flag "--output_mode EMIT_ALL_SITES" but...
When I tried to call variants using the command line like following: Program Args: -T UnifiedGenotyper -nt 4 -R mm10.fa -I PWD.bam -I la215.bam -I la210.bam -o output_chr14.vcf -L chr14...
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 ArticleMerging Genome VCF's for the Same individual
Hi this is pretty much a feature request for something I think would be useful, I mentioned it briefly at the Brussels workshop and it seems like it might be possible. In a couple of projects I'm...
View ArticleHow can I solve "No overlapping contigs found" error for PhaseByTransmission...
I'm trying to run PhaseByTransmission but I have issues. I converted my plink file in vcf format and I downloaded the GRCh38 files (.fasta, .dict and .fai) from the google cloud. When I run GATK I get...
View ArticleGATK 3.0 HaplotypeCaller RUNTIME ERROR
Hi, I am running Haplotypecaller for ~600 bams to perform gVCF call on a cluster (SGE qsub system). Each node has 32 cores, 256 GB RAM. I am running 8 tasks pernode, so each task has 4 cores and 32GB...
View ArticleCombineGVCFs warn messages into GVCF output??
Hi, I just switched to GATK 3.6 because of the bug in CombineGVCFs reported at http://gatkforums.broadinstitute.org/gatk/discussion/comment/31641#Comment_31641 I have noticed that now the CombineGVCFs...
View ArticleMuTect2 with Queue
Hi, I'm trying to run Mutect2 with matched normal-tumor whole genome samples and I want to use Queue. I know it will take a lot of time with WGS samples and I want to use Queue as mentioned here...
View ArticleMutect2 long runtime issue
Hi, I have been running Mutect2 on WES, till now it ran for 40 hours, and the vcf file only has till chromosome 7. I ran Mutect2 on a 32GB node and with 12 cores. My question is more like can Queue be...
View ArticleThe mannual scatter-gather of BQSR output differs from gatk-queue BQSR...
Hi, I tried to run BQSR 32 times parrallely each with a contig I specified using -L option, there are no spaces between the contigs, then I gathered the reports with GatherBqsrReports tool. The output...
View ArticleRerun using different reference
Dear Sir/Madam! We have discovered a problem in our data generated using the best practice pipeline for variant calling (GATK 2.7.2, bwa 0.7.4, picard 1.92). We originally used the hg19 reference...
View ArticleMutect is not working
Dear Cancer team, I installed mvn, gatk-protected, and mutect. (https://github.com/broadinstitute/mutect) After that, I came upon the following error message: ERROR...
View ArticleA question about a weird output of VCF file from UnitedGenotyper
When I call variants using UnitedGenotyper, usually, the 9th column of a vcf file would be GT:AD:DP:GQ:PL and it indicate the information that the following columns have. But when I called variants...
View ArticleGathered bam could not be indexed
Hi, I runed indelRealigner of the same bam for 32 times each with a -L option which specify an interval, then I gathered the bam files of the outputs using picard GatherBamFiles(I found that the gather...
View ArticleHelp with samtools problem "Error parsing text SAM file. MAPQ should be 0 for...
Hello, I am trying to convert a sam file to bam and am getting the below error. Can you help me with how I can fix this? Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing...
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...
View ArticleVariant not called by GATK
Hi there, I am doing alignment using Novoalign and using best GATK (version 3.5) practice to call variant. Sample is NA12878. One of my expected variant at location chrX:31219271 is not called. I ran...
View ArticleDiagnoseTargets only output low-coverage intervals?
I am using DiagnoseTargets on whole exon sequence data. Even though in the output .vcf file, it mentioned several filters (such as BAD_MATE, COVERAGE_GAPS, LOW_COVERAGE,NO_READS,PASS,POOR_QUALITY), I...
View ArticleFS question
Hi there, gVCF files dont have FS or SOR in Info column. X 32503194 . T C, 4947.77 ....
View ArticleBug with version 3.6 and jexl
I recently tried to use a GaTK command I previously used with GaTK 3.5, and I'm getting a jexl error. I don't understand why. I've updated to java 1.8.0_77 java -Xmx${MEM} -jar...
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