problem with FastaAlternateReferenceMaker
Hi, I'm trying to use FastaAlternateReferenceMaker to generate an alternate reference from VCFs files. Unfortunately I get an error message: ERROR MESSAGE: Input files variant and sequence have...
View Articlehow I interpret the genotype result?
Dear all, Follow the GATK best practice, I got one sample with the genotype 0/0:47,0:49:99:0|1:131931451_TA_T:0,141,1807 in the vcf file. According to the format column GT:AD:DP:GQ:PGT:PID:PL, this...
View ArticleHow do SelectVariants and VariantEval handle spanning deletion "*"?
Hi, I have recently used GATK 3.5 to run joint calling (GenotypeGVCFs). After that, I used SelectVariants to select one sample and ran VariantEval with the sample's data. However, I am curious about...
View ArticleHaplotypeCaller generates diff results on different CPUs
I encountered an interesting problem: running HaplotypeCaller on different machines generates different result for 2 sites. The machines use the same input BAM file, same reference, same java...
View ArticleMutect variant calling the parameters for filtering
Hello All, I have a couple of vcf files resulted from a batch run from the pipeline from the Mutect and I wanted to filter the output cf file based on the following parameters...
View ArticleInterpreting Allele frequency equal to 1.0
Hi, In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never...
View ArticleWhere might I download an hapmap for experimenting with GATK
Error messages beaucoup attend the use of VariantsToVCF tool in the following command line: java -jar gatk.jar -T VariantsToVCF -R reference.fa -o output1.vcf --variant:RawHapMap input.hapmap Having...
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 ArticleWhy does GATK LeftAlignAndTrimVariants set a missing genotype to 0/0?
Hi. I appreciate many your helps. I have one vcf file (a.vcf). This file has one variant data. The data also has missing genotypes "./." because of DP=0. The variant is tri-allelic variant as below....
View ArticleMultisample SNP Calling
Hello! I'm trying to use GATK to call SNPs on multiple bam files (at once) but I encounter some "problems". I tried HaplotypeCaller and UnifiedGenotyper and it works well. The vcf is generated. But not...
View ArticleAllele Depth = '0,0' and DP = '0' but the mutation was passed by filter
Hello, There is a question if anyone can explain to me how this variant calling was made, and why it was passed by filter. A variant information in filtered VCF is: 10 118265356 . G A 152.03 PASS...
View ArticleMuTect 2 Output lacking of AD information for Tumor sample
Greetings: I have been working on a WES data, and managed to finished my first round of MuTect2. (Though I used the option -nct 4, it still tack almost 10 days for MuTect2 to finish the analyze.) Below...
View ArticleConvert 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 ArticleFastaAlternateReferenceMaker giving error
Hi, I am trying to run FastaAlternateReferenceMaker using an interval file but I am getting this warning whether I use the interval file or not. java -jar /local/scratch/aparihar/GenomeAnalysisTK.jar...
View ArticleThresholds for variants filtering
Hi all, I would like to ask about thresholds used to filter out variants. What thresholds should I use and why ? I appreciate any help, Thank you.
View ArticleGenotypeGVCFs java error; java.lang.NegativeArraySizeException
Hello! I used the following command to run GATK GenotypeGVCFs. (GATK version : nightly-2016-11-23-g69e703d / Java : Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14)...
View ArticleMuTect2 sample names
My MuTect2 VCF records header looks like this: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL The samples are named TUMOR and NORMAL rather than by the actual names. It doesn't appear like...
View ArticleRemoving overlapping variants from one VCF file from another?
Hello! Firstly let me say the support in this forum is amazing and we are very lucky to have you guys listen and respond to our issues! I have illumina DNA sequening of bacterial populations which are...
View ArticleVCF file malformed
Hi all. I am new in bioinformatics. Now I am trying to do a base re calibration and this is why I need a dbsnp.vcf with the known variants of the genome I am working. I downloaded the dbsnp file from...
View ArticleSelectVariants Large VCF slow runtime
I am attempting to subset and filter a large (10k exome sample, 250GB) VCF file using SelectVariants. My goal is to subset by individual samples (iterating over each sample using a custom script and...
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