Convert Mutect1 output to VCF
Hi Geraldine & Sheila, I have run Mutect1 (1.1.7) on whole genome sequences and got the output as a text file. Is there a way to convert this to VCF? I found out now that one can specify --vcf...
View ArticleHaplotypeCaller Error on some bam files
Hello GATK team, I report an error using HaplotypCaller on 3 bam files (other 34 bam files were processed without problem) Exemple: $ nohup /opt/java/jre1.8.0_102/bin/java -jar...
View ArticleHow can we identify between the missing SNP (because of insufficent coverage)...
Hi, I had 11 samples for which i ran GATK (BQSR and VQSR), is there any way to differentiate between missing SNP (because of insufficent coverage) and homozygotic SNPs Thanking you in anticipation....
View ArticleRNAseq variant calling from HISAT and Trinity aligners
Hi guys, I want to perform variant calling on my RNAseq dataset and I got stuck at the Split'N'Trim pre-processing step, as I want to apply the same (or similar) pipeline to two sets of reads: 1....
View ArticlecombineGVCF batch effects
Dear Sir/Madam, We have been using the best practice variant calling pipeline to call variants in our targeted sequencing data (GATK 3.2.2). Me and others in the team have discovered batch effects in...
View ArticleLogging error when connecting to ftp server
Hello! i am trying to run the following command to download the dbsnp_138.b37.vcf.gz and i get a login erro. following my command and error message. am I making any mistakes or the server is having a...
View ArticleWhere to download the HLA caller?
I am trying to download as you explain here: http://gatkforums.broadinstitute.org/gatk/discussion/65/hla-caller but I cannot find it.
View ArticleGATK realigner
Hi, I used the below command "java -Xmx2g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ref.fa -I lib_sorted.bam -o lib.intervals -nt INT" to run my data, but the program stoped when running...
View ArticleERROR MESSAGE: Unable to read index file, for input source:
Hi,GATK term I have set up a bwa + gatk best pratices pipeline for variant calling on pannel data(700 samples ). I use the haplotype caller in gvcf mode.The bam to the gvcf commands is : java -Xmx20g...
View ArticleERROR MESSAGE: Code exception (see stack trace for error itself)
Hi,GATK term I have set up a bwa + gatk best pratices pipeline for variant calling on WES data (50 samples ). I use the haplotype caller in gvcf mode.When I joint gvcf to vcf with the following...
View ArticleMuTect2 Haplotypes
Hi, I am struggling to figure out, how MuTect2 calculates allele frequencies. Based on a previous problem [1] caused by non-deterministic calls when run on multiple CPU cores, I have decided to run...
View ArticleHow to get heterozygotes SNP with HaplotypeCaller ?
Hi, I am new to GATK, I try to find SNPs for paired-end data in the mosquito. The genome of the mosquito many polymorphism. I try to get a VCF file for each position all posibility for a SNP. In fact,...
View Articletumor cohort versus normal cohort variation comparison
Dear GATK group, We aim to compare snp/indel differences between a tumor cohort and a normal cohort. Going through your documents, we see GATK tumor/normal pair branch, which seems to be based on one...
View ArticleDetermining ploidy via read ratios with HaplotypeCaller: skewed results?
Hello, I am attempting to determine the ploidy of my organism by observing where the modes of SNP allele ratios fall. For example, a 2N diploid should have a peak of allele read-counts at 0.5 since...
View ArticleWhat's in the resource bundle and how can I get it?
NOTE: we are currently working on overhauling the bundle to 1) add support for Hg38 and 2) document the provenance of the resource files more fully. 1. Accessing the bundle See the Resource Bundle...
View ArticleDescription and examples of the steps in the CNV case and CNV PoN creation...
The CNV case and PoN workflows (description and examples) Requirements Java 1.8 A functioning GATK4-protected jar (hellbender-protected.jar or gatk-protected.jar) HDF5 1.8.13 The location of the...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencer when it estimates the quality score of each base...
View Articlemutect2 filter fieild
Hello, We found a mutation was tagged as "PASS" in FILTER field with mutect2 (3.6 version) for some samples, however, this mutation is in our Panel of normal. For some other samples, this mutation was...
View ArticleExclude unescaped quote marks from GATK header?
I've recently run into an error running a pipeline on GATK SelectVariants-generated VCFs. The issue seems to be that SelectVariants (and perhaps other tools) leaves header line(s) containing multiple...
View ArticleFiltering VCF file Based on BED file
Hello, I recently downloaded a VCF file from NIIST and was trying to filter out based on the my BED file. Do I use "select variant" or "Filter variant" command? It would be great if you can help me...
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