Clik here to view.
Extremely high depth of coverage
Dear all, I've run the DepthOfCoverage tool on 263 WGS samples and have found some unusual total and averages for some regions. Does it mean any sort of error on the alignment or I can just filtered...
View ArticleCalculateGenotypePosteriors and pedigree file
I am trying to use the CalculateGenotypePosteriors tool using only family priors. I understand that the pedigree file should be in plink format. I have two large half-sib families with RAD-Seq data. So...
View ArticleWhich training sets / arguments should I use for running VQSR?
This document describes the resource datasets and arguments that we recommend for use in the two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration), based on...
View ArticleWhile using HaplotypeCaller not enough memory
I am using the HaplotypeCaller but I am getting the error not enough memory to run this program java -jar -Xmx8g /home/manager/Downloads/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T HaplotypeCaller -R...
View Articleerror in compilation of SortSam using Queue
Hello, I have been trying to run SortSam using Queue on my data (using this sample code here: http://gatkforums.broadinstitute.org/gatk/discussion/3293/scala-script-for-running-queue) When I try the...
View ArticleClik here to view.
LeftAlignAndTrimVariants --splitMultiallelics changes GT from known to unknown
I have a VCF file with this line (i.e. GT=0/1=G/T): 20 10120854 . G T,A 32175.56 . AC=399,18;AF=0.111,5.006e-03;AN=3596;BaseQRankSum=1...
View ArticleGATK command for adding known vcf file for SNP's so as to filter it out
Hi, I want to add a known vcf file of snps maybe from one of the databases of snp and want to remove those snp's if they also occur in my sample. How can I do this in GATK. Also I am interested in...
View ArticleMESSAGE: Unable to create iterator for rod named variant in GenotypeGVCFs
Hi all, I tried everything I can do, but can not find the solution. Any help will be appreciated. PROGRAM DETAILS: GATK version: GATK v3.6-0-g89b7209 Program Args: -T GenotypeGVCFs -D dbsnp_137.b37.vcf...
View ArticleSplitNCigarReads complains about N in CIGAR
I am working on RNAseq data. I expect SplitNCigarReads can handel spliced reads, but it complains about N in CIGAR. I just wonder whether SplitNCigarReads is ready to handle spliced reads or still...
View ArticleGATK licensing through Broad starts today
It’s official! As of today, we are able to offer commercial licenses for GATK and MuTect directly through Broad. Stay tuned for details of terms & conditions, coming soon to this very blog. In the...
View ArticleAny way to restrict HaplotypeCaller to work only on a set of regions?
Hi, for diagnostic purposes, I would like to run HaplotypeCaller on very small regions (even just a single base locus). I thought that was what the -AR switch was for, so I have: java -jar...
View ArticleCan we implement GATK/Queue on google hadoop?
Hello, I`m new to GATK and Queue. I understand that we can write a QScript in Queue to generate separate GATK jobs and run them on a cluster of several nodes. Can we implement GATK or Queue on google...
View ArticleSNPs not filtered out in hard filtering
Hi! I hope you can give me some help or advice on the hard filtering of the SNPs. I'm working on the lovebird genome and my reference genome is a young male (we did the assembly) and its parents are...
View ArticleA question about using GenomeAnalysisTK to deal with ancient DNA data
Hi,Team, I want to call variants for some ancient samples using HaplotypeCaller. My command is as follows: java -jar GenomeAnalysisTK.jar -R myref.fa -T HaplotypeCaller -ERC BP_RESOLUTION -I 1.bam -L...
View ArticleLimit on number of samples that can be handled in the joint calling pipeline
Hello, I have not tried testing the limit yet on the number of samples for the joint calling pipeline (i.e., HaplotypeCaller in GVCF mode, CombineGVCFs and GenotypeGVCFs) but do you guys allready know...
View ArticleGet all VCF files in proper format?
Hi, I tried running the following command to generate the VCF file using Haplotype Caller java -jar GenomeAnalysisTK.jar -T HaplotypeCaller --dbsnp chr7.vcf -R chr7.fa -I chr7.bam -A AlleleBalance...
View ArticleFile number limit for GenotypeGVCFs
Hi there: I'm trying to figure out if I need to run CombineGVCFs before GenotypeGVCFs. The documentation said "One would use this tool when needing to genotype too large a number of individual gVCFs"....
View ArticleGuidelines for using CombineGVCFs
Hi, In the documentation for CombineGVCFs it says: CombineGVCFs is meant to be used for hierarchical merging of gVCFs that will eventually be input into GenotypeGVCFs. One would use this tool when...
View ArticleReduce mutect running time
I'm running mutect-1.1.7.jar using java 1.7 on the dutch-lsgrid and it runs longer than the limit imposed of 72 hours wall time as it cannot run in parallel. How can I reduce the running time by using...
View ArticleUndergraduate Research using Neutral Theory, Tajima's D (somewhat), and SNPs
Hi everyone, I'm going to explain my undergraduate research and I hope you can tell me if this bioinformatics software will help me. So basically my question states, "Is asthma a modern ailment (due to...
View Article