GenomeAnalysistk.jar's option
hi. I brought a question today. I am not good at English. I'm sorry. GenomeAnalysisTK.jar -T... what's mean -T? and BaseRecalibrator -R, what's mean -R? if that question already was existed, I'm so...
View ArticleOncotator 1.9.2 wrong annotation
Dear oncotator team I have recently updated to oncotator version 1.9.2 and oncotator_v1_ds_April052016 database. The tool got installed properly and is running fine without any error. But, the output...
View ArticleMapping, processing and duplicate marking with Picard tools: ValidateSamFile...
I am trying to follow the best practices for mapping my (Paired-end Illumina HiSeq) reads to the reference, by following this presentation: From what I understand, I should use MergeBamAlignment to...
View ArticleCross comparison between Array and NGS data
Dear GATK staff, I have a 11 samples that were sequenced using NGS (Illumina HiSeq) and 2 of these samples were also genotyped using an Illumina Human Global screening array (Illumina Iscan). I was...
View ArticleHaplotypeCaller 3.5 keeps crashing
We use HaplotypeCaller ver. 3.5 in a trio analysis (having three persons - mother, father and child, WES, paired-end). HC is scattered per chromosome, so we have 25 jobs for each person (75 in total)....
View ArticleSelectVariants modifies VCF entries, keeping only the base calls intact.
I am using GATKv3.5. I used SelectVariants as shown below to remove 11 samples from a vcf file: java -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fasta -V all_samples.vcf -xl_sn sample90...
View ArticleSelectVariants -env doesn't remove all non-variant sites
I am using GATKv3.7, trying to remove a few samples from a big VCF file and remove all invariant sites. Here is the code I ran: java -jar GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar -T SelectVariants...
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(How to) Generate an unmapped BAM from FASTQ or aligned BAM
Here we outline how to generate an unmapped BAM (uBAM) from either a FASTQ or aligned BAM file. We use Picard's FastqToSam to convert a FASTQ (Option A) or Picard's RevertSam to convert an aligned BAM...
View Articletrio pipeline
Dear friends I am analyzing a trio I have followed the pipeline described in van der Auwera et al. 2013 on each person individually up to HaplotypeCaller and VariantRecalibrator is there a pipeline I...
View Article(howto) Get started with GATK4 beta
Download the software The GATK4 beta version command-line tools are provided as a single executable jar file. You can download a zipped package containing the jar file from this Github link (GATK4...
View ArticleHow can Mutect2 GATK 4 beta be parallelized?
Hello, I am creating PoN for Mutect2 and following an instruction in the comments of Mutect2.java gatk-launch --javaOptions "-Xmx4g" Mutect2 \ -R ref_fasta.fa \ -I normal1.bam \ -tumor...
View ArticleWhy do BAM files have to be correctly formatted before Picard RevertSam?
Hi all, After completing tutorial #6483 on mapping and cleaning up short read data efficiently, I tried this with our lab's own BAM files. However, when completing the first step (generate a uBAM from...
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Malformed walker argument
Hello, I installed GATK package as explained in the documentation, but I am not able to use the "walkers" with go with it. I always this error message: java -jar GenomeAnalysisTK.jar -T IndelRealigner...
View Articlepicard of CollectVariantCallingMetrics error
[Thu Jun 29 17:13:02 CST 2017] picard.vcf.CollectVariantCallingMetrics INPUT=BGIyaozu.qc.vcf OUTPUT=BGIyaozu DBSNP=dbsnp_138.hg19.vcf GVCF_INPUT=false THREAD_COUNT=1 VERBOSITY=INFO QUIET=false...
View ArticleUsing Queue vs. WDL scatter
I'm attempting to figure out what's the difference between using gatk-queue vs using wdl-scatter for parallel.
View ArticleWhere can I find additional documentation for gatk-queue
I'm reading through the documentation here, and setup/ran Maven to build project. However the documentation makes the following assertion java -jar dist/Queue.jar --help im unable to find any dist/...
View ArticleClean version of dbSNP in the GATK resource bundle
Hi I understand that version 129 of dbSNP is considered clean and does not share data from other databases such as 1000G projects. What steps of the variant calling in WGS/WES analysis can be affected...
View ArticleErrors about input files having missing or incompatible contigs
These errors occur when the names or sizes of contigs don't match between input files. This is a classic problem that typically happens when you get some files from collaborators, you try to use them...
View ArticleHow do I create a metadata(.fam) file for the VariantsToBinaryPed function?
I am new to working with genomics data, and I haven't been able to find any helpful instruction on how to create a metadata file for the VariantsToBinaryPed function. It seems counter-intuitive that...
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