VCF file is malformed at approximately line number - GATK ASEReadCounter
Dear GATK Team, While running GATK ASEReadCounter using 3.4 and 3.7, i am getting errors related to known sites vcf file. As per article I have done alignment and processed bam file....
View ArticleMergeBamAlignment Failure
Hello, I'm trying to use Picard 2.9.0 MergeBamAlignment, but get this error: Command: $ java -jar /data/murphy/shared_bins/picard-tools-2.9.0/picard.jar MergeBamAlignment...
View ArticleMuTect2 ->Reference name for '1283' not found in sequence dictionary
Hi, I am trying to run java -jar GenomeAnalysisTK.jar -T MuTect2 -R ucsc.hg19.fasta -I:tumor tumor_rg.bam -I:normal normal_rg.bam -o output.vcf I am using ucsc.hg19.fasta as a reference and I used: 1....
View ArticleGATK Runtime Error on GenotypeGVCFs: java.lang.Double cannot be cast to...
Hi GATK Team, I've run into the following error when trying to genotype ~1200 GVCFs: java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.Integer I've replicated this error on...
View ArticleWhat is the significance of "Depth across all samples" (DP) in INFO ?
Hi, Although I have read through the related topics, I'm still quite confused about the significance of "Depth across all samples" (DP) in INFO in the vcf file. Does "across samples" mean it addition...
View ArticleQuestions about BQSR (2014-2016)
This discussion was created from comments split from: Base Quality Score Recalibration (BQSR).
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Bug in HaplotypeCaller：GT is called “./.”，but AD and DP isn't 0
HI, I'd like to report a weird result from HaplotypeCaller. We have a patient sequenced by targeted sequencing,We expected to see no heterozygous variants called in this locus,it have found the insert...
View ArticlelibVectorLoglessPairHMM is not present in GATK 3.8 - HaplotypeCaller is...
We are running GATK on a multi-core Intel Xeon that does not have AVX. We have just upgraded from running 3.4-46 to running 3.8, and HaplotypeCaller runs much more slowly. I noticed that our logs used...
View ArticleHow to create an indexed VCF for BaseRecalibrator?
First, I searched the forum for answers to my question, but none of them seem to be working. I have a non-model organism and I'm trying to use BaseRecalibrator as recommended in the manual: run the...
View ArticleMuTect2 not found using GATK version 3.8 and Java 1.8
Hi, I receive an error of not finding MuTect2 when trying to run it with GATK version 3.8 and Java 1.8. Please, find below the Java version: java version "1.8.0_112" Java(TM) SE Runtime Environment...
View ArticleService note: forum on break, support resumes Nov 27
Today in the US we're celebrating the national "Stuffing Your Face" holiday known as Thanksgiving, and we get the day off tomorrow to recover, so the forum is going to be unattended until Monday Nov...
View ArticleWhy do half of my variants get rejected in picard LiftoverVcf?
Dear team, You may not be providing support for picard, but at least the LiftoverVCF tool is referred to several places in this forum. I am working on two batches of bam-level data from the same...
View Articlet_lod_fstar big value
t_lod_fstar is a probability value, because my values are above a thousand? Example: t_lod_fstar 982.172809 2812.706107 1818.586417 899.623243 736.025622 3239.922082 3242.985246
View ArticleQuestion when I use FastqToSam to confert my fast Q files to sam files
Hi, I have the problem when I use the FastqToSam to convert my fastqfiles to sam files, I use the latest picard version. I use the command line below: java -jar picard.jar FastqToSam...
View ArticleHalf of my variants get rejected by using picard LiftoverVcf
Hi, I want to include samples which are aligned on b37 and hg19 for genotypeGVCFs and VQSR with b37. I have used picard LiftoverVCF on gvcf files with hg19tob37.chain. But 60% of variants are rejected...
View ArticleVQSR: Bad input: Values for DP annotation not detected for ANY training...
Hi team, I'm have a vcf callset file generated using HaplotypeCaller in --emitRefConfidence GVCF mode with subsequent GenotypeGVCFs. I used the generated output.vcf file as input for...
View ArticleIMPORTANT -- Bug alert for GATK4 GenomicsDBImport
We have identified a major bug in the GenomicsDBImport tool that affects all released beta versions of GATK4 up to 4.beta.5 (inclusive). The bug occurs under specific conditions (detailed below) and...
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 ArticleWhen there is a GATK update, when do you know if you should rerun old data?
When there is a new version of GATK released, how do you know whether it is necessary to rerun all of your old data for an ongoing project? I realize there is probably not one good answer to this...
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