Dangling heads and tails
Hello, The logic for merging dangling tails appears to be different from that for dangling heads. For example, it looks like tails can be merged to a non-reference path while heads cannot. Is there a...
View ArticleHow to indicate --fraction_contamination in MuTectV1 using results from ContEst
Dear GATK/MuTect team, I'm attempting a somatic WES using MuTect V1. I ran ContEst on a trial matched normal and tumor co-aligned bam respectively, and obtained 3.1% for normal, 0.8% for tumour. 1) May...
View ArticleERROR MESSAGE: Unable to read index file, for input source:
Hi,GATK term I have set up a bwa + gatk best pratices pipeline for variant calling on pannel data(700 samples ). I use the haplotype caller in gvcf mode.The bam to the gvcf commands is : java -Xmx20g...
View ArticleDoes IndelRealigner work the same way as the indel realignment included in...
Hello GATK Team, I wonder if IndelRealigner work the same way as the indel realignment included in HaplotypeCaller. Do they use the same algorithm? Does this mean that I don't need to realign indel for...
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 ArticleMutect2 output with samples with different read groups
Hi all, I am running Mutect2 with a tumour/normal match in RNA-Seq. Here is my command: gatk -T MuTect2 -R ./genome.fa --read_filter Mappin gQuality --min_mapping_quality_score 20...
View ArticleMalformed VCF file
Hello I am using BisSNP-0.82.2 tool to find SNP in bisulfite data. But I get the below mention error while using this command : java -Xmx4g -jar BisSNP-0.82.2.jar -R...
View ArticleCan GATK use a gtf file?
I'm running GATK to extract SNPs from RNAseq data. I used this command to split reads into exons and hard clip any intronic regions. java -jar GenomeAnalysisTK.jar -T SplitNCigarReads -R ${REF} -I...
View ArticleIs Mutect2 missing from GATK 3.7?
if I try to give -T MuTect2 to the gatk jar, I get the following: Invalid command line: Malformed walker argument: Could not find walker with name: MuTect2
View ArticleFastaAlternateReferenceMaker creates different size fastas from same reference
Hi all, I am using FastaAlternateReferenceMaker to insert all SNPs from an already filtered VCF file into a reference to create a new consensus sequence for each sample. The functions all run without...
View ArticleGATK for Nanopore data
Hi, I'm trying to use GATK to perform variant calling analysis with Minion Nanopore data. In details, I would like to ask you if someone has already used GATK to analyse Nanopore sequencing data, and...
View ArticleIs scatter gather based on interval lists causing problems for GatherBamFiles?
I'm running GatherBamFiles on shards from PrintReads that were generated using the intervals that I have attached to this post. I created the intervals with the python script that's available on your...
View Articlethe metrics file creation in picard tools producing empty file
bwa mem -x pacbio assembly.fa PacBio_raw.fastq > aln.sam samtools view -b -S aln.sam -o aln.bam samtools sort aln.bam > aln_sorted.bam java -jar /share/apps/picard-tools-1.56/MarkDuplicates.jar...
View ArticleHow can I access the GSA public FTP server?
How can I access the GSA public FTP server?
View ArticleSome questions about VQSR.
Can I ask three questions about VQSR: 1. I have two VCF files from two different sources, and each of them contains several samples. The sequencing processes are basically the same (library prep,...
View ArticleError in "-T AnalyzeCovariates -before *.recal_data.table -after...
INFO 08:34:15,496 GenomeAnalysisEngine - Strictness is SILENT INFO 08:34:15,572 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 08:34:15,647...
View ArticleBest Practices for Batch Calling Malaria
Since there is no gold standard SNP database for Plasmodium vivax, my lab and I have been tinkering with a pipeline for variant calling with GATK. I'm pretty confident with the basic framework we have,...
View ArticleIndelRealigner problems
when I ran the IndelRealigner command, I caught up with the question --"MESSAGE: Error caching SAM record FCD054AACXX:4:2102:2977:12785#TTAGGCAT, which is usually caused by malformed SAM/BAM files in...
View ArticleQuestions about Indel Realignment (2012-2013)
This discussion was created from comments split from: Local Realignment around Indels.
View ArticleQuality score
Hi! I have followed all the steps in the variant discovery part of the guidelines and had to apply hard filters because I'm working on a non-model organism. My question is if you could perhaps help me...
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