NON_REF in gvcf
I see something like this chr1 17697 . G C, 72.77 . BaseQRankSum=0.322;ClippingRankSum=-1.517;DP=8;MLEAC=1,0;MLEAF=0 .500,0.00;MQ=40.00;MQ0=0;MQRankSum=0.322;ReadPosRankSum=0.956 GT:AD:DP:GQ:PL:SB...
View Articleoutputing genotype after variants are called
Hi, How do I output the sample's genotype (including non-variants) after I ran the pipeline and got the vcf file? Thanks!
View ArticleHow to read a SAM record into the SAMRecord class
Hello, I am trying to read in Array[htsjdk.samtools.SAMRecord] into the SAMRecord class and trying to get their starting position by the getAlignmentStart method of the class. I have created the...
View ArticleDebug message from htsjdk.samtools.FixBAMFile
I use htsjdk.samtools.FixBAMFile to fix occasional bin errors when use BWA-backtrack with old datasets: java -cp htsjdk.jar htsjdk.samtools.FixBAMFile source.bam fixed.bam This bin fixing issue is...
View ArticleRevertSam in picards
I need to re-map two kinds of BAMS: a) the re-calibrated BAMs and b) hg19 mapped BAMs to hg38. I am looking into the GATK tutorial:...
View ArticleGenotypeGVCFs requires a reference
Hi all, I am trying to do joint genotyping from .gvcf files produced separately per sample, through the command line java -Xmx4g -jar /bio/GenomeAnalysisTK.jar -T GenotypeGVCFs -V...
View ArticleHaplotypeCaller error: bad variant representation and missing variant in gvcf...
Hi all, I'm using GATK v.3.6 for a multi-sample analysis. I followed best practices and this is the command line for HaplotypeCaller: java -Xmx64g -jar $GATK -T HaplotypeCaller \ -R $REF \ -I...
View ArticleCan you consider updating /bundle/2.8/b37/human_g1k_v37_decoy.fasta.fai.gz?
Hi GATK team, I found that using 'human_g1k_v37_decoy.fasta.fai' with samtools1.2 gives a floating point exception after a look at the fai indexes of human_g1k_v37_decoy.fasta.fai and...
View ArticleInvalid JEXL expression detected
Hi, I am attempting to filter a combined vcf file with 400 samples based on several FORMAT fields in gatk 3.6.0 (latest overnight update). I have previously achieved this step with a different data set...
View ArticleIs there some special advise for construct PON of single tumor cell?
Did I must use single normal cell to construct PON for tumor cell? Could i use bulk sample to construct PON? Thanks
View ArticleHow much Memory would GATK Tools HaplotypeCaller, GenotypeGVCFs, and MuTect2...
I am running these tools on WES data, bam size is about 20G. How much memory would be enough to run these tools? Is MuTect2 the only tool among the 3 that is recommended to use multithread? What would...
View ArticleERROR MESSAGE: Bad input:We encountered a non-standard non-IUPAC base in the...
Hi, I'm currently working with bwa, samtools and GATK to make SNP calling on Medicago truncatula. I'm using my own reference sequence, with the 8 chromosoms in the same fasta file. C1_lenght=155648...
View ArticleInbreeding coefficient
Hi GATK team, I have a question about VQSR. For "VariantRecalibrator" I used as annotations: -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -tranche 100.0...
View ArticleShoud I run GATK tool GenotypeGVCFs by batch
I have WES data from several batches for one project. Should I run GATK tool GenotypeGVCFs on all normal samples, or should I run it by batch? In order to check sample swap with verifyBamID, I need...
View ArticlePicard tools MarkDuplicates without swap usage
Hi, I've been trying to run MarkDuplicates on a shared cluster and I keep getting the job killed because of swap usage. I'm trying to figure out a way to use MarkDuplicates without just throwing tonnes...
View ArticleHaplotypeCaller prints empty VCF file
I am trying to do variant-only calling for DNA sequence using the following command: java -Xmx5120m -jar GenomeAnalysisTK.jar -T HaplotypeCaller -nct 4 -R ucsc.hg19.fasta -I region0-3.bam -o...
View ArticleIs there a way to automatically get nighly builds
Dear GATK team, i maintain GATK on the NIH biowulf cluster (https://hpc.nih.gov/apps/GATK.html). We have all recent stable builds available. However, sometimes users ask for a nightly builds b/c of...
View ArticleHaplotypeCaller fails on joint calling of gVCFs
Hi, when I run HaplotypeCaller on on a bunch of .g.vcf files, at the joint discovery stage, it creates the output vcf with the header, but doesn't output the variants. There are a couple of warnings I...
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Bug in HaplotypeCaller: GT is called 0/1, but AD is 206,0
HI, I'd like to report a weird result from HaplotypeCaller. We have a patient sequenced by targeted sequencing on HNF1B. This patient has been confirmed to have a whole gene deletion of HNF1B so we...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
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