Version highlights for GATK version 3.6
What better way to start the summer than with a new GATK release? Umm no don't answer that, there's loads of good options. You could have a barbecue, eat some ice cream, go on a hike if that's the sort...
View Articlecalling variants on haploid organism
Hi, I'm curious about something I find using HaplotypeCaller on my haploid fungus. (using it with -ploidy 1) In my vcf there are some variants with low variant allele frequency (around 50%). for...
View ArticleGATK4 CNV Runs on Indivisual Set, How Can I tell Which Segments are Somatic
As the title, GATK4 tool CNV runs on individual set, then how can I tell which CNVs are somatic. Usually there are always some errors, the germline CNVs sometime are not identical in paired samples....
View ArticleMutect2 output file variant to table
Hi, I used mutect2 to call somatic SNP/Indels for my paired tumor sample. When I used the following command to extract mutations, I found half of mutations with dbsnp rs # which can be found in the...
View Article1000Genomes vcf file and correct reference genome used in...
I am using a vcf file from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ Specifically, chromosome 20. 1000Genomes says their reference genome is GRCh37, which is the same as hg19. However,...
View ArticleGenotypeGVCFs wgs samples
I have about 130 wgs vcf files (created by GATK HaplotypeCaller). When I try to use GenotypeGVCFs, it goes out of memory. Can I split the sample vcf files by chromosome, call using GenotypeGVCFs, and...
View ArticleConflict between HaplotypeCaller variant and BAM
Hello, I'm using GATK version 3.6 to analyze a trio exome, and I followed the best practices (prinseq, bwa, markduplicates, baseRecal, printReads, HC and hard filtering, to resume the pipeline; with...
View ArticleBug 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 ArticleIndelRealigner/RealignerTargetCreator known site bundle files
Hi, For both IndelRealigner/RealignerTargetCreator, there is an option for known indel sites as below: -known /path/to/indels.vcf However, from the bundle files collection such as from hg19, there are...
View ArticleRequest for key for GATK versions before 3.6
Hi GATK team, I would like to request for a GATK key to bypass the "Phone Home" feature. May i seek your advice how i could go about to acquire the key? Thank you so much. Regards, Michelle L.
View ArticleFastaAlternateReferenceMaker -- how to create the two fasta version of a...
Hi there, I have been struggling recently with my data. Indeed I have aligned my individuals to a reference fasta and now I have a vcf. Thanks to FastaAlternateReferenceMaker I can generate the...
View ArticleHow to interpret output of EstimateLibraryComplexity
Dear all, I am quite knew to the analysis of RNA-seq data and was searching the www for an answer relating to the interpreation of the results outputted by Estimate_libraryComplexity. The only...
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 ArticleInteractive map of the global GATK user community
This morning, we unveiled an interactive GoogleMap, based on anonymized IP addresses collected from the forum database, that shows how the GATK user community is distributed across the globe. Check out...
View ArticleError encountered first Base Recalibration step
Hi GATK team, I've encountered an error at base recalibrator step (1st round) and below is the snapshot of the error. =========================== INFO 12:19:25,364 ProgressMeter - [INITIALIZATION...
View ArticleMutect2 - Ploidy setting also for normals?
Dear I have a question regarding the ploidy setting of the mutect2. I have two whole-exome sequencing datasets of a tumor sample – both treated under different conditions. The goal is to find genetic...
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Errors in SAM/BAM files can be diagnosed with ValidateSamFile
The problem You're trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn't clearly tell you what's wrong. Bits of the stack trace (the pile...
View ArticleHow many processor and memory space required for paired end RNA seq data...
Hi All, I would like to do GATK RNA seq analysis for paired end data set. I would like to know what are the minimum required cores for running the job. please help me Thanks, AkilaRanjith
View ArticleWhen should I use -L to pass in a list of intervals?
The -L argument (short for --intervals) enables you to restrict your analysis to specific intervals instead of running over the whole genome. Using this argument can have important consequences for...
View ArticleGATK error
Any help figuring out this error is appreciated; trying out this variant calling workflow and I begin here with already removed duplicate reads and I'm trying realigning the bam file: Removed duplicate...
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