How to filter out the SNPs with deletion allel ?
Hi, I'm wondering whether there are a way to filter out the SNPs with deletion allel (*). I'm just not confident enough to keep these snps so I prefer rather discard them rather than having false snp....
View Articleevaluate SNPcalling
I did SNP calling with samtools mpileup and now I want to produce some stats about my SNPs to make filtering. my samples are from a great tit (Parus major). I tried to used VariantEval tool but for...
View ArticleGenotypeGVCFs error
Hi I am getting the following error. I ran the exact same samples/pipeline a couple of weeks ago using 3.6 and it worked fine, now with 3.7 I am getting an error: INFO 09:49:49,742 HelpFormatter -...
View ArticleMuTect Output for 2 consecutive nucleotide substitution
For on patient, if there is nucleotide substitution on 2 consecutive location, MuTect gives results as if they are 2 different mutation from different cells in the same patient. Problem with this is if...
View ArticlePrinciple of removing duplicated reads in Picard
MarkDuplicates of Picard is a useful function to remove duplicated reads. However, after reading the introduction of Picard...
View ArticleInstallation v1.9.2.0 on Ubuntu 14.04.05 failed systematically
Hi, We try to install oncotator latest release (v1.9.2.0) on a Ubuntu 14.04.5 LTS. But failed First python setup.py install failed due to some reason So we have installed all dependancies manually as...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencer when it estimates the quality score of each base...
View ArticleHow should I pre-process data from multiplexed sequencing and multi-library...
Our Best Practices pre-processing documentation assumes a simple experimental design in which you have one set of input sequence files (forward/reverse or interleaved FASTQ, or unmapped uBAM) per...
View ArticleWhat is the best practice for calling/combining variants across multiple...
Hi, I am working with RNA-Seq data from 6 different samples. Part of my research is to identify novel polymorphisms. I have generated a filtered vcf file for each sample. I would like to now combine...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleHaplotypecaller: Problem with using ploidy argument.
Dear GATK team, I tried to fix the ploidy issue with sex chromosome in my pipeline, based on the information that I got from the previously asked questions. However, when I run that, there is No...
View ArticleVersion highlights for GATK version 3.1
This may seem crazy considering we released the big 3.0 version not two weeks ago, but yes, we have a new version for you already! It's a bit of a special case because this release is all about the...
View ArticleCombineVariants - duplicate reads are generated for the same chr:pos
I am merging two VCFs. the records are as below VCF1: CHROM POS ID REF ALT QUAL 1 1247578 . TG TGG,TGGG,TGGGG,TGGGGG,T,TGGGGGG 53367.32 VCF2: CHROM POS ID REF ALT QUAL 1 1247578 . TG...
View ArticleKnown sites for indel realignment and BQSR in hg38 bundle
Dear GATK team, I'd like to learn what files I should use for indel realignment and BQSR from hg38 bundle? (I read the manual on this topic -- https://broadinstitute.org/gatk/guide/article?id=1247 --...
View ArticleHow to select insertion or deletion from a indels vcf file?
Hi, I have a InDels vcf file which contains both insertions and deletions. I would like to select only insertions or only deletions from this InDels vcf file using the following command line. $ java...
View ArticleRemove duplicate reads from ChIP-seq data
In general, the reads un-mapped to reference, multiple-alignment, and duplicated, should be removed after mapping to reference in ChIP-seq pipeline. The source of PCR duplicated includes...
View ArticleERROR stack trace Code exception
Hi I am running the RealignerTargetCreator and I am having the next problem: INFO 22:02:18,183 HelpFormatter - -------------------------------------------------------------------------------- INFO...
View ArticleName Tag Error while running Base Recaliberator
Hi! I am running into an error while running BaseRecaliberator, I also googled it up and tried a lot of suggestion but nothing helped. Here is what I am doing: java -jar GenomeAnalysisTK.jar -T...
View ArticleAt what point should I merge read group BAM files belonging to the same...
It is fairly common to have multiple read groups for a sample, either from sequencing multiple libraries or from spreading a library across multiple lanes. It seems this causes a lot of confusion, and...
View ArticleCollectHsMetrics for merged bams
Dear all, I am using PICARD version 2.1.1 to generate metrics for my samples. The samples were sequenced with llumina NextSeq, we loaded a single library that is a pool of 12 samples. The flow cell has...
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