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Missing or Inconsistent call between single-sample and multi-sample SNP calling
Dear all, I have generated a gVCF file using HaplotypeCaller (v3.7)and searched for a specific variant of interest which looks like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N417 chr1 627033...
View ArticleQD Annotation error in GATK in VariantRecalibration step
hi all, i downloaded a BAM file from 1000 genomes to work on and converted it to FASTQ and aligned with bwa mem to hg38, this worked fine. later I wanted to run VariantRecalibration and use the...
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Spanning or overlapping deletions (* allele)
We use the term spanning deletion or overlapping deletion to refer to a deletion that spans a position of interest. The presence of a spanning deletion affects how we can represent genotypes at any...
View ArticleMissing field QD in vc variant (ERROR)
Hello! I'm trying to extract SNPs of interest from my filtered VCF file of passing SNPs. I just used SelectVariants to create that file, and am now trying to use VariantsToTable to put them into a...
View ArticleDifferences between CollectFragmentCounts and CalculateTargetCoverage
Good afternoon, I was hoping somebody could help illuminate the differences/similarities between CollectFragmentCounts (4.0 official release) and CalculateTargetCoverage (4.3 Beta). Are these the same...
View ArticlePloidy level in HaplotypeCaller in GATK 4.0
Hi, Thanks for the new version of GATK (GATK4.0). We have a pooling of 48 samples and the organism is diploid, we are using ploidy of 96 (48x2=96). earlier when I am using HaplotypeCaller for variant...
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 Articlepicard ./gradlew test error
I have an error when tried to run ./gradle tests on my system. I am running Linux Mint 18 system. Could you please let me know what should I do? Thank you. $ java -version openjdk version "1.8.0_151"...
View Article[ERROR] GATK4 Mutect2
Hi, I want to call mutations for my WGS data. But, the workflow for one of my pairs is failed. I got the following ERROR message in MergeVcfs task. It seems that one of the VCF files is not in correct...
View Article[ERROR] make_acnv_pon_config
Hi, I want build a CNV PoN by "make_acnv_pon_config". But, I got a message as following. Any suggestions? Thanks a lot! I will really appreciate your help. Failures: message: Task...
View ArticleHaplotypeCaller warnings DepthPerSampleHC
Hi I'm trying to do a multisample variant call using several bam files in the following cmd /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa...
View Article-nct not present in GATK 4.0.0.0
Hi, Is --native-pair-hmm-threads in GATK 4.0.0.0 same as -nct in older GATK versions?
View Articleno. of cores utilization in haplotypcaller in GVCF mode
Hi, I am running Haplotypecaller (v4.0.1.2) (not the spark version) on some WGS samples on a SGE (Sun grid Engine) cluster. When I am submitting a job to my cluster, I am asking for 1 core (on an 8...
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Variant calls in mixed samples - HaplotypeCaller GVCF
I have a question about the behavior of HaplotypeCaller when used incorrectly Specifically, how would it call variants from a diploid sequence if the ploidy was set to 1? Would it simply call the most...
View Articleunmapped BAM from Ion 16s Metagenomics Kit using MergeBamAlignment
I have sequenced 16s rRNA from waste water samples using Ion 16s Metagenomics kit. After paired-end sequencing using the machine Ion S5, I have received unmapped BAM files for all samples. Each uBAM...
View ArticleGATK4 Realign around indels
Hi, Looking through GATK4 best practices for pre-processing fastq files and do not see a "realign around indels" ( in GATK3 : java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator ) . Should I use...
View ArticleVariantsToBinaryPed java.lang.ArrayIndexOutOfBoundsException: -1
Hello, can you please help me sort out the following error in running VariantsToBinaryPed: java -jar /sb/project/fkr-592-aa/data/GalWaRat/bin/third/gatk-3.7/GenomeAnalysisTK.jar -T VariantsToBinaryPed...
View ArticleNeed clarification on Picard CollectHsMetrics (ZERO_CVG_TARGETS_PCT)
I used Picard CollectHsMetrics on whole exome data of 96 individuals. We used xGen® Exome Research Panel v1.0 exome capture kit. 1) In the output file ZERO_CVG_TARGETS_PCT ranges from 37-41. The...
View ArticleRecommendation Interval length for genomicsdb import
Dear GATK Team Is there any recommendations for the length of one interval specified in genomicsdb import? I am running a genomicsdb import for about 50 bam samples (from cattles) for whole length of...
View ArticleVariantAnnotator is not annotating variants with InbreedingCoeff
Hi, I am using GATK VariantAnnotator to annotate my VCF with the InbreedingCoeff but when I check the output VCF I see that no variant was annotated with the InbreedingCoeff. I've used a pedigree file...
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