Tag: VQSR

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GATK 4.3.0 VQSR 1 Hi all, With GATK4.3.0 I try to use VQSR and I got the error message. Based on GATK tem recommendations, I ran “VariantRecalibrator model” to fix the error gatk.broadinstitute.org/hc/en-us/articles/9570271608219-VariantAnnotator. However. the error message still persists. Is there any other way to fix such problem? Thanks! A…

Hi all, I am working with GATK version 4.3.0. I am a bit confused which code can I used for VQSR and ApplyVQSR. I found the code for ApplyVQSR on gatk.broadinstitute.org/hc/en-us/articles/9570419503259-ApplyVQSR while for the first step (VQSR) I did not find the code for the version am using it. In…

CNNScoreVariants Error 0 Hello guys, I have a problem with CNNScoreVariants code. When I use the code : gatk CNNScoreVariants \ -V input.vcf \ -R reference.fasta \ -O annotated.vcf It has given the error : !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: CNNScoreVariants is an EXPERIMENTAL tool and should not be used for production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!…

Demographics Data from three studies were included: Dan-NICAD: 1,649 individuals with symptoms of obstructive coronary artery disease, predominantly chest pain, undergoing coronary computed tomography angiography. In total, 52% were females, the mean age was 57 years (+/- 9 SD), median coronary artery calcium score were 0 [0–82] and 24% of…

My following command java -Xmx10g -Djava.io.tmpdir=Varcalling/cohort.vcf_VQSR -jar gatk-package-4.0.1.2-local.jar VariantRecalibrator -R /xxx/REFERENCES/hg19//bwa_index/hg19.fa -V Varcalling/cohort.vcf -resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0 /xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf -resource omni,known=false,training=true,truth=false,prior=12.0 /xxx/REFERENCES/hg19//1000G_omni2.5.hg19.sites.reorder.vcf -resource dbsnp,known=true,training=false,truth=false,prior=6.0 /xxx//REFERENCES/hg19//dbsnp_138.hg19.reorder.vcf -resource 1000G,known=false,training=true,truth=false,prior=10.0 /xxx//REFERENCES/hg19//1000G_phase1.snps.high_confidence.hg19.sites.reorder.vcf -an SOR -an QD -an MQRankSum -an ReadPosRankSum -an MQ -an FS -an DP -mode SNP -O Varcalling/cohort.vcf.SNP.recal –tranches-file Varcalling/cohort.vcf.SNP.tranches –rscript-file Varcalling/cohort.vcf.SNP.plots.R gives an error…

Can not generate tranches plot after VQSR 0 Hello! I have encountered with a strange issue when trying to analyze VariantRecalibrator output. I can not generate or find an R-script file of *.tranche output. At the same time i have no problems with scatter-plots generation an further import in Rstudio….

Hello. After running my codes for VQSR’s first step, I receive all files (including R scripte for plots) except the pdf file that contains plots. I do not have any errors from the vqsr. My code: java -jar gatk-package-4.3.0.0-local.jar VariantRecalibrator \ -O /home/yousef/Desktop/VQSR_hg38/haplotype_hg38_SNP_Recal.vcf \ –resource:hapmap,known=false,training=true,truth=true,prior=15.0 ‘/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/Coverted_to_VCF/Coverted_broad_hg38_v0_hapmap_3.3.hg38.vcf’ \ –resource:omni,known=false,training=true,truth=false,prior=12.0 ‘/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/Coverted_to_VCF/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf’ \…

Error in VQSR first step 0 Hello. After inserting following codes for VQSR first step: java -jar gatk-package-4.3.0.0-local.jar VariantRecalibrator -O /home/yousef/Desktop/haplotype_hg38_SNP_Recal.vcf –resource:hapmap,known=false,training=true,truth=true,prior=15.0 ‘/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/resources_broad_hg38_v0_hapmap_3.3.hg38.vcf’ –resource:omni,known=false,training=true,truth=false,prior=12.0 ‘/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf’ –resource:1000G,known=false,training=true,truth=false,prior=10.0 ‘/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf’ –resource:dbsnp,known=true,training=false,truth=false,prior=2.0 ‘/media/yousef/EEFC0BDBFC0B9CC9/Sequencing/Next_generation_sequencing/Index_files/VQSR_data/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf’ –tranches-file /home/yousef/Desktop/Tranches.txt -an QD -an SOR -an MQ -an FS -an SOR -an ReadPosRankSum -an MQRankSum -V /home/yousef/Desktop/haplotype.hg38.vcf –max-gaussians 4 -R…

Hello In the first step of BQSR I get the following error. How should I fix it? At the end of message, I have written my code to perform this task. A USER ERROR has occurred: Contig chrKI270728.1 not present in the sequence dictionary [chr1, chr10, chr11, chr11_KI270721v1_random, chr12, chr13,…

Downloading required resources for VQSR 0 Hello. During VQSR, we need to introduce files with known mutations and variants to train the machine. Can you please tell me the website that I can download following file for this purpose? 1000G omni- indel/SNP hapmap hg19 dbsnp_138 CEUTrio.Hiseq.WGS WGS.WES sequencing genome VQSR…

Hi everyone, I am currently working on a medium-sized WES cohort study and wanted to know what the bioinformatics community would regard a cutting-edge workflow. As the big labs usually utilize GATK I also started with that. The results for SNPs are ok, but manual inspection (IGV) still uncovers a…

Variant quality and filters on GATK HaplotypeCaller generated VCFs 0 Hi, I am analysing human WGS data to diagnose rare inherited diseases. I followed the GATK Best Practices Guidelines for “Germline short variants discovery” for single-sample data to generate a VCF using HaplotypeCaller. The guidelines then point to the use…

Expected Behavior Filter the calls from HaplotypeCaller with Variant Quality Score Recalibration according to GATK best practise (Tools VariantRecalibrator, ApplyRecalibration, see gatkforums.broadinstitute.org/gatk/discussion/39/variant-quality-score-recalibration-vqsr or a more recent version) Current Behavior Variant quality score recalibration currently not included. Asked Jan 26 ’18 at 08:25 malinlarsson 1 Answer: Keep in mind, that you’d…

gnomAD v3 link not working for download 1 your URL is wrong. $ wget -q -O – “https://storage.googleapis.com/gcp-public-data–gnomad/release/3.1.1/vcf/genomes/gnomad.genomes.v3.1.1.sites.chr1.vcf.bgz” | gunzip -c | head ##fileformat=VCFv4.2 ##hailversion=0.2.64-1ef70187dc78 ##FILTER=<ID=AC0,Description=”Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)”> ##FILTER=<ID=AS_VQSR,Description=”Failed VQSR filtering…