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Calling variants in RNAseq
Overview This document describes the details of the GATK Best Practices workflow for SNP and indel calling on RNAseq data. Please note that any command lines are only given as example of how the tools...
View ArticleCan't download resource data of oncotator
Hi all, I failed to download resource data provided by README and cann't on the Internet. Could someone post the correct links here. Thanks very much. Here are the three failed links....
View ArticleSeveral Annotations not working in GATK Haplotype Caller
I am using Genotype Given Allele with Haplotype Caller I am trying to explicitely request all annotations that the documentation says are compatible with the Haplotype caller (and that make sense for a...
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What is a GVCF and how is it different from a 'regular' VCF?
Overview GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF (see the spec documentation here), but a Genomic VCF contains extra...
View ArticleMuTect2 and multiple read groups per sample, issue with index
I have an issue with BAM files containing multiple read groups for the same sample (identical SM:), essentially this is the same situation as my MuTect1 related question form 2 years ago:...
View ArticleGQ Score Weirdness (zero vs. 99)
I hope this question is appropriate for this particular forum. I am tracking down some SNP calls between two identical samples to see why they were labeled SNPs so that I can improve my filtering after...
View ArticleMuTect2: A Strange question on allele depth
Hello, I have to admit the way I used MuTect2 is quite unorthodox and probably not strictly supported, but the problem I ran into is one of inconsistent read depth, which I don't think to have much to...
View ArticleHaplotypeCaller - different versions & code exception
Dear GATK team Now I am trying to run HaplotypeCaller to call SNPs on the realigned bam files from a poplar species, and use the genome of Populus trichocarpa as reference. The coverage of different...
View ArticleHaplotypeCaller Code exception & different version
Dear GATK team Now I am trying to run HaplotypeCaller to call SNPs on the realigned bam files from a poplar species, and use the genome of Populus trichocarpa as reference. The coverage of different...
View Article(howto) Run the GATK for the first time
NOTICE: This tutorial is slightly out of date so the output is a little different. We'll update this soon, but in the meantime, don't freak out if you get a result that reads something like INFO...
View ArticleCombineGVCFs error
Hi, I am getting error message "Problem detecting index type" while combining 200 GVCFs generated by HaplotypeCaller (gatk 3.5). Can you suggest how can i identify source of this error or if this is...
View ArticleFunctionality request
I wonder whether it's possible to have a parameter to suppress the commandline from the output of SelectVariants and VariantFiltration? If I use JEXLs in these functions, and if those JEXLs have double...
View ArticleGATK haplotype caller: discrepancy between AD and GT
Hi We have come across a few calls as below, where the winning PL and genotype point to 0/1, yet the AD shows zero reads supporting the ALT allele. Is this expected, or is it a bug? chr1 726136 . TGGAA...
View Article(howto) Recalibrate base quality scores = run BQSR
Objective Recalibrate base quality scores in order to correct sequencing errors and other experimental artifacts. Prerequisites TBD Steps Analyze patterns of covariation in the sequence dataset Do a...
View ArticleWhy the candidate like this is rejected? It seems to meet all requirements.
contig position context ref_allele alt_allele tumor_name normal_name score dbsnp_site covered power tumor_power normal_power total_pairs improper_pairs map_Q0_reads t_lod_fstar tumor_f...
View ArticlePurpose and operation of Read-backed Phasing
This document describes the underlying concepts of physical phasing as applied in the ReadBackedPhasing tool. For a complete, detailed argument reference, refer to the tool documentation page. Note...
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A fatal error has been detected by the Java Runtime Environment when using...
Hi, I used MuTect2 for somatic SNV and indels calling and tested 9 tumor and matched normal WGS samples. ../jdk1.8.0_91/bin/java -jar ../GenomeAnalysisTK-3.6.jar -T MuTect2 -R...
View Articlehow to build/get populationAlleleFrequencies.vcf for ContEst
How to build/get populationAlleleFrequencies.vcf for ContEst ? and what is the necessary field of VCF file? AF field? MAF field? I found no guide for this. and I tried 1000G vcf file, but it failed...
View ArticleError with CollectWgsMetrics
I get errors trying to run CollectWgsMetics similar to a previous post (http://gatkforums.broadinstitute.org/dsde/discussion/6692/error-while-using-collectwgsmetrics). It appears to have run, but it...
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...
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