Bug Report -- VariantsToTable
VariantsToTable allows you to use "-SMA" to split multi-allelic variants into multiple rows. I am trying to work it on ExAC vcf (0.3.1) files. It works for AC, AN field in the INFO tag, but not for...
View ArticleHaplotypeCaller fails on joint calling of gVCFs
Hi, when I run HaplotypeCaller on on a bunch of .g.vcf files, at the joint discovery stage, it creates the output vcf with the header, but doesn't output the variants. There are a couple of warnings I...
View ArticleWhat is the source of the runtime error when using HaplotypeCaller?
Greetings, I am attempting to use the HaplotypeCaller using GATK version 3.6 and received a Runtime Error. The command I used was: Java –jar GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -R $chicken.fa \...
View Articlecan't access the bundle ftp page
Hi, I am using my username and password to access the bundle page, but it does not accept my username/password. I clicked on the URL on this article:...
View Article(howto) Apply hard filters to a call set
Objective Apply hard filters to a variant callset that is too small for VQSR or for which truth/training sets are not available. Caveat This document is intended to illustrate how to compose and run...
View ArticleMissed SNPs downstream of intronic repetitive context
I've found some interesting behavior in HaplotypeCaller in GATK 3.6 that I was hoping someone would help explain. I have a sequence context with 3 phased SNPs directly downstream of an intronic...
View ArticleCombineGVCFs performance
I've got 300 gvcfs as a results of a Queue pipeline, that I want to combine. When I run CombineGVCFs (GATK v3.1-1) this however seems fairly slow: INFO 15:24:22,100 ProgressMeter - Location...
View ArticlegenotypeGVCF
Hi there, I used -ERC gVCF mode in Haplotyper to call variant on single sample. One of the variants listed below is present in gCVF file. I then used genotypeGVF to convert the gcvf fie to vcf file and...
View ArticleGATK BaseRecalibrator complaining about sort order of VCF file that is sorted...
I am running GATK's BaseRecalibrator with 2 input .vcf files with known SNPs. Both of these VCF files have been sorted using picardtools SortVcf Upon visual inspection, both VCF files are sorted...
View ArticleHomozygous indels in haplotype caller
Hi, I'm trying to understand certain homozygous indel calls from HaplotypeCaller (v 3-3-0) on the human genome. These calls have the following properties (from the gatk bamout file unless otherwise...
View ArticlePicard (2.1.0): the CollectHsMetrics discrepancy
Hi everyone, I'm having trouble understanding some results using CollectHSMetrics from Picard's latest version (2.1.0). It seems like the values i'm getting for MEAN_BAIT_COVERAGE and...
View ArticleBase Recalibration with non-model organism
I've been following the guidelines for how to generate the known sites SNP database for organisms for which none already exists. I used my entire sample set (66 samples) to generate a VCF SNP file,...
View ArticleGATK error
Hi,all; When I run the following command /bin/java/jre1.7.0_55/bin/java -Xmx2G -Djava.io.tmpdir=./java_tmp -jar /bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T UnifiedGenotyper -R...
View ArticleGenomestrip CNV results wonky
Hi @bhandsaker The results of CNVdiscovery followed by compute allele frequencies, are a bit weird for me. I've attached two IGV images, showing both the genomestrip vcf file, and bam files from two of...
View ArticleQuestions about the resource bundle (continued)
This discussion was created from comments split from: What's in the resource bundle and how can I get it?.
View ArticleUnable to access jarfile /GenomeAnalysisTK.jar
First of all, did not find exact name "Java 1.8.x" on the Ubuntu Software Center. I had to search the web to finally get a program called Java Platform (JDK). Would be good to give some more info on...
View ArticleStatus for dealing with paired-end reads
Hi all, new here and its my first post, so sorry if its not relevant enough. I have been thinking about the same problem that occurred here twice already, and i cannot seem to come to a conclusion on...
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9 Takeaways to help you get started with GRCh38
We are starting official support of GRCh38, a reference genome with alternate contigs. In fact, going forward all of our new projects will use GRCh38. During this transition over the coming year, we...
View Articlewhat are -nt and -nct for parameters?
Hello, what kind of parameters are -nt and -nct? Thanks a lot.
View ArticleERROR MESSAGE: java.lang.Integer cannot be cast to java.lang.Double
Hi, after running 5 exomes with GATK-v3.3 and HaplotypeCaller, I encountered a very low titv ration in my samples (~2.1) as VaraintEval report indicated. I tried running varaint filtration in these...
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