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Support team appreciation day -- say hi and get a prize
I want to give mad props to my team. Every day they handle new questions about obscure error messages or unusual experimental designs, on top of their ongoing efforts to develop new documentation...
View ArticleASEReadCounter contruct a heterozygous VCF input file for all nucleotides in...
The aim is to identify any and all bi-allelic SNPs in my region of interest. Then determine if there is allelic imbalance in all my RNA-seq samples. I already filtered the BAM files for the region of...
View ArticleException when processing alignment for BAM index
I used the SplitNCigarReads with the following command. java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R test.fasta -I sorted2.bam -o sorted2_split.bam -rf ReassignOneMappingQuality -RMQF 255...
View ArticlePicard Sort Vcf Error
Hello. I am using GATK version 3.6, picard-2.8.2.jar I downloaded hapmap_3.3.hg38.vcf from gatk resource bundle. I then used the below command to remove chr notation. awk '{gsub(/^chr/,""); print}'...
View ArticleHaplotypeCaller calling as heterozygotes incorrectly
I am finding that HaplotypeCaller is calling heterozygotes when there is no evidence when you look in IGV. Is this still a known problem? I am using version 2.8-1-g932cd3a. Attached are two screen...
View ArticleWhich one should I use for ContEst --popFile?
http://gatkforums.broadinstitute.org/gatk/discussion/6687/how-to-build-get-populationallelefrequencies-vcf-for-contest says I should use...
View ArticleDetection of somatic mutations with RNAseq - Mutect2
Hello, We are working on a swine model of melanoma, where tumors trigger an efficient immune response, most likely by producing neoantigens, ie proteins carrying somatic mutations and thereby...
View ArticleGATK HaplotypeCaller Error: Java stack error
I get the same error repetitively while running GATK HaplotypeCaller (see below). This seems to occur around the same chromosome positions for each of the 3 bam samples. Rest of the samples run without...
View Article"ArithmeticException" in VariantFiltration and "Invalid JEXL expression...
Hi, I have been trying get variants out of a VCF file where the Allele Frequency (AF) is greater than 4%. I have tried both VariantFiltration and SelectVariants but I get different errors with each....
View ArticleDoes HaplotypeCaller block the bam and/or reference while it is running?
I have been trying to speed up HaplotypeCaller by running multiple instances on the same bam file, but with different intervals provided to each instance through the -L option. We are wrapping our...
View ArticleMost efficient way to combine multiple GVCF files
Dear GATK team, In order to calculate variant frequencies, all samples from different runs must be in the same GVCF. For each run, I'am currently running the CombineGVCF tool and then I use the...
View Articlehow to build/get populationAlleleFrequencies.vcf for ContEst
How to build/get populationAlleleFrequencies.vcf for ContEst ? and what is the necessary field of VCF file? AF field? MAF field? I found no guide for this. and I tried 1000G vcf file, but it failed...
View ArticleContEst：what if I do not have a genotype array of my nomal samples?
Hi, I want to use ContEst to estimate the contamination levels of my patient-matched normal samples, but all my data are WGS data, and I dot not have genotype array of my normal samples. My code is...
View ArticleVCF header with AD format 'Number=R' causes error in VQSR VariantRecalibrator...
I have a VCF header with the following number annotation for the AD field: ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">...
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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 ArticledbIndel as input for Mutect2
Hello, I was wondering if Mutect2 accepts a "dbIndel" as input. Something similar to the "--dbsnp" argument, but for known Indels. I am currently using GATK bundle hg38 files in my Mutect2 pipeline :...
View ArticleAnnotating vcf with dbSNP IDs: Indel problem
Hi team, I'm trying to replace my in-house identifiers with those from dbSNP. I've done this before with a purely SNP dataset by applying GATK AnnotateVariants, and then using bash to change the column...
View ArticleGATK 3.7 HaplotypeCaller NullPointerException in...
HaplotypeCaller in GATK 3.7 (3.7-0-g56f2c1a) is throwing a NullPointerException in some cases. See below for log output from a failing run. It looks to me like the call to .get() in the...
View ArticleMESSAGE: BUG: requested unknown contig=ERCC-00002 index=-1
Hi, I'm currently running variant calling on RNA-SEQ data from the ENCODE Project. To streamline the process, I have downloaded their previously aligned RNA-SEQ data (they used STAR aligner.) I then...
View ArticleActual Genomes-in-the-Cloud Docker Container
Hi, I see you published a new Version on DockerHub (Version 2.2.5) with a recent version of bwa (0.7.15-r1140 instead of 0.7.13-r1126). Would it be impertinent to ask if you can put recent version of...
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