Empty VCF files using UnifiedGenotyper
Hi, I must be doing something silly because all of my VCF files are empty (header, no results) after calling with Unified Genotyper. I'm using GATK version 2.7-2-g6bda569 with Java 1.7.00_40. The...
View ArticleQC of genotypes
How I can remove SNPs with Low quality or out of Hardy-Weinberg in my VCF file. In column 7 of my VCF file I have only "LowQual" or ".". There is no "PASS" word in this column. Is there something wrong...
View ArticleError Stack trace after running SelectVariants
I just wanted to select variants from a VCF with 42 samples. After 3 hours I got the following Error. How to fix this? please advise. Thanks I had the same problem when I used "VQSR". How can I fix...
View ArticleHow to calculate the GQ of a SNP?
Hi, I'm trying to understand how do you usually calculate the GQ of a SNP. I understood the model to calculate the Likelihood of all the genotypes (AA,AC, AG,AT,CC,CG,CT,GG,GT,TT). Once all the...
View Articlecalling SNPs with pooled samples using UnifiedGenotyper
I using the UnifiedGenotyper to call SNPs in a pooled sample of 30 diploid individuals (i.e., I am setting the ploidy to 60). Does this mean that if the coverage is < 60 at a given variant site, the...
View ArticleRare variants from annotated vcf file
Hi, I have annotated my vcf file of 20 samples from Unified genotyper using the following steps. Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator My question is...
View ArticleCan compression of VCFs (when specifying output file as .vcf.gz) be improved?
This is not a bug per se in that it does not cause incorrect output, but I think it would be accurately described as an "unintended consequence" of very poorly compressed VCF output files. GATK allows...
View ArticlePossible bug in CombineVariants
I believe that I may have found an issue with the CombineVariants tool of GATK that manifests itself when there is a repeated ID in a given VCF. For us, the reason to have repeated IDs in a VCF file is...
View ArticleFastaAlternateReferenceMaker missing some indels
Dear all I am writing to you to understand why FastaAlternateReferenceMaker is missing a deletion in the final consensus. I am using gatk v. 2.8-1 and this commandline: gatk -R ref.fa -T...
View ArticleHelp with genotyping in my vcf file
Dear GATK team, Could you please help me how to explain genotyping in my vcf file. I have Illumina data and vcf caller was GATK. My variant frequency (Alt variant freq) is 99.7%. DP = 4622 (AD = 16,...
View ArticleReads in RodWalkers
RodWalkers are really fast and great. Is there any way to connect a BAM file to it and get the pileup in the given positions? If not, what is the appropriate way to get pileups for a small set of...
View ArticleHow do I direct Queue to output files to a different directory?
Hi, Thanks to previous replies can run Queue and the relevant walker on a distributed computing server. The question was if I define my scala script to require an argument for the output file, using...
View ArticleBug: Haplotype Caller Odd VCF files
Hi I've just been having a go with the new Haplotype Caller method and I've getting some odd or malformed lines in the VCF file for example: For example the format line has declared we should have 4...
View ArticleIdentifying good SNPs
Hi, I start working with IGV, but I have some doubts in how to identify a good SPN in this program. First I download the new Soybean Genome on Phytozome (Gmax_275_v2.0.fa and...
View ArticleRealignerTargetCreator parameter -known [File] fails when creating .idx file.
Hi, I'm trying to use the RealignerTargetCreator as a test with 1 know file; 1000G_phase1.indels.b37.vcf. At first the contigs didn't match with my .BAM file (chr1/chr2 vs 1/2), so I adjusted that. Now...
View ArticleInclude no-calls in vcf with only variant sites
Is there a way to include only variant sites and no-calls in your final vcf. I know during SNP calls you can only emit variants, or only confident sites or all. However is there a way to reduce your...
View ArticleSelect Certain Number of Random Variants
Is there a Walker to select a certain number of random variants from a VCF file? I have checked only the SelectVariants, but the only option similar is --select_random_fraction, that select a fraction...
View Articleformat fields and sample entries in VCF files
I've noticed a small bug with GATK tools and VCF files. CombineVariants and GenotypeGVCF can generate files where some samples have fewer fields than the format column. For instance, this is part of a...
View ArticleDoes BaseRecalibrator require a vcf file ?
Hello I am following the gatk best practices guide, and using the 2 stages BaseRecalibrator process. The first recalibration is going well, the second one, produces an error like described below, I...
View ArticleThe provided VCF file is malformed at approximately line number 37:...
Hi! I try run GATK with SelectVariants. But the error message was generated. ERROR MESSAGE: The provided VCF file is malformed at approximately line number 37: unparsable vcf record with allele X My...
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