Tag: VQSR

priced – VQSR.com | NamePros

VQSR.com Registered in 12 extensions!! Potential client: vqsr.academy Price : $220 REG: GoDaddyEXP: 7/1/2024 Payment options : WISE, PAYPAL F&F, ACH Transfer, SEPA Transfer, Escrow, DAN, DAAZ.Accepted payment in EUR and USD.Prices in EUR are calculated in real time exchange rate.Transfer method: Push, Auth CodeThe buyer is responsible to cover…

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priced – VQSR.com, igjl.com | NamePros

VQSR.com Registered in 12 extensions!! Price : $300 REG: GoDaddyEXP: 7/1/2024—————————————————————————————————-igjl.com Price : $200 REG: SAVEXP: 30/11/2024—————————————————————————————————- Payment options : WISE, PAYPAL F&F, ACH Transfer, SEPA Transfer, Escrow, DAN, DAAZ.Accepted payment in EUR and USD.Prices in EUR are calculated in real time exchange rate.Transfer method: Push, Auth CodeThe buyer is…

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GATK 4.3.0 VQSR

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…

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GATK4.3.0

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…

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CNNScoreVariants Error

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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!…

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DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals | BMC Genomic Data

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…

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GATK4 VariantRecalibrator resource error

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…

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Can not generate tranches plot after VQSR

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….

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VQSR first step do not generating plots

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’ \…

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Error in VQSR first step

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…

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How to fix “Contig chrKI270728.1 not present in the sequence dictionary ” error

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,…

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Downloading required resources for VQSR

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…

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GATK vs DeepVariant : bioinformatics

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…

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Variant quality and filters on GATK HaplotypeCaller generated VCFs

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…

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Do VQSR for HaplotypeCaller calls – Sarek

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…

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gnomAD v3 link not working for download

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…

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