Picard Optical Duplicates calculation 2.0 vs 2.1+
Hi, We have an old pipeline that has been running with Picard 1.141 and reporting various metrics including optical dupes in our Illumina data. I'm just upgrading it to use Picard 2.8.1 and I see that...
View ArticleWhat does an error message mean?
Overview This document lists error messages that you may encounter when using Oncotator. For each, you will find an explanation of what the error message means, and how to solve the problem (if...
View ArticleI need help. GATK Haplotypecaller says my dict is empty but it isn't??
The Error message I get is the following INFO 12:25:14,659 HelpFormatter - ---------------------------------------------------------------------------------- INFO 12:25:14,662 HelpFormatter - The...
View ArticlePhasing
Hi there How do u incorporate phasing with your variants if you dont have data from parents. my haplotype output is 1/1 not 1|1 so how can we say haplotyper can give phased haplotypes. Huma
View ArticleHow to compare two vcf files of two cultivars?
Hi, I am looking for a program that could help to compare two vcf files of two cultivars. I have three vcf files (vcf1, vcf2, vcf3) of SNPs of three different cultivars. The SNPs were called using...
View ArticleGATK4 Plot segmented coverage
Hello I am using GATK4 for detecting CNV in 143 genes. Everything works great except for the plots, i found no errors in the command line but i dont know why all the plots appear empty. i checked all...
View ArticleGenotypeGVCFs will give a stack trace if using -nct > 1 and -allSites
Hi, I'm getting a NullPointerException (see trace below looks like some kind of NanoScheduler issue) when using GenotypeGVCFs and the -allSites argument when using more than one core via -nct. Running...
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Attend or host a GATK workshop to see what's cooking
GATK workshops bring you the latest in our methods development. The materials we prepare for workshops often serve as a base for our documentation on new or improved tools and workflows. So not only do...
View ArticleTargeted RNA-seq: using ASEReadCounter
We have used a targeted sequencing approach to sequence 70 genes of interest from n=24 liver samples for ASE analysis both at gDNA level (for variant calling) and cDNA from RNA (for ASE). We used the...
View Articlemultiple fastq files for a sample produced same number of columns in vcf, how...
Hello, I have multiple sequence files for a sample: sample1: 1.fastq; 2.fastq, 3.fastq sample2: 4.fastq; 5.fastq I did the alignment with CLC genomics and called SNPs with GATK. The input was two...
View ArticleMuTect2 sample names
My MuTect2 VCF records header looks like this: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL The samples are named TUMOR and NORMAL rather than by the actual names. It doesn't appear like...
View ArticleError with SamTools in GATK 4 CNV Proportional Coverage
Hi, I am attempting to run the GATK4 CNV Proportional Coverage task, but an error occurred in one of my samples. I've attached the stderr file. The relevant part seems to be there is an issue in a...
View ArticleOld version of GATK
I installed GATK3.7 but could not run since I have an old java version 1.7.0_122. I would very much like to update my Java and run GATK3.7, however I do not have administer permission of our server....
View Article[E::bwa_idx_load_from_disk] fail to locate the index files
Hello, I tried to execute the command line in putty (linux) as follows: $ bwa mem -M -t 8 Homo_sapiens_assembly38.fasta SRR1517898_1.fastq SRR1517898_2.fastq > SRR1517898.sam but this appears:...
View ArticleGATK 4 CNV Proportional Coverage for WGS : Firehose task "ERROR SparkUI:...
Hi - Today I've been trying to use the "GATK 4 CNV Proportional Coverage for WGS " (version 4) task in Firehose copied from Algorithms Commons. After 16 warnings: WARN Utils: Service 'SparkUI' could...
View ArticleVQSR - ./. genotypes retained after VQSR filtering
We have generated a set of variant calls based on the GRCh38 pipeline described in GATK using GATK version 3.3. We observed that many calls made on the ALT contigs had the genotype call "./." . On...
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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 ArticleGenotypeGVCF crashes ?
For what a reason the GenotypeGVCFs crashes at the same position on chr4 (only for chr4). below is the error message. any hint on this ? thanks LSBATCH: User input java -Xmx64g...
View ArticleSPlitNCigarReads: endless memory hunger
Hi, When using SPlitNCigarReads on a 15GB mRNA .bam file, the program keeps being stuck at the same progression no matter the memory amount I supply to it. Command line used: java -jar...
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...
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