[GATK 4.0.0.0] CollectRnaSeqMetrics --IGNORE_SEQUENCE as required argument?
Hi, I have been using an old version of PicardTools for some time and I have only recently decided to move to GATK4, mostly due to the improvements in performance. Upon doing so I have noticed that...
View ArticleExit codes in GATK 4.0
Hi, In my BASH scripts I often use "$?" to monitor the exit status of a process and normally stop if there is an error. However, I am using the latest version of GATK (4.0.0.0) and some tools return 0...
View ArticlelibVectorLoglessPairHMM is not present in GATK 3.8 - HaplotypeCaller is...
We are running GATK on a multi-core Intel Xeon that does not have AVX. We have just upgraded from running 3.4-46 to running 3.8, and HaplotypeCaller runs much more slowly. I noticed that our logs used...
View Articleprebuilt gatk4 does not show --list on OSX HighSierra+java9
Hi there, Is it possible that mac and or java 9 are not happy with the gatk wrapper? Thanks in advance Stephane $ gatk --list Using GATK jar /opt/biotools/gatk-4.0.0.0/gatk-package-4.0.0.0-local.jar...
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 ArticleIntroduction to the GATK Best Practices
This document provides important context information about how the GATK Best Practices are developed and what are their limitations. Contents What are the GATK Best Practices? Analysis phases...
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Run the germline GATK Best Practices Pipeline for $5 per genome
By Eric Banks, Director, Data Sciences Platform at the Broad Institute Last week I wrote about our efforts to develop a data processing pipeline specification that would eliminate batch effects, in...
View ArticleTroubleshooting: ERROR - variant files have inconsistent references for the...
Greetings, I am hoping to get some help troubleshooting a frustrating error I am having trying to genotype a large set of data. The source data is nearly 12000 WES samples, which were sequenced by a...
View ArticleTrouble with Best Practices
Hi I'am new with all NGS tools, I tried to follow best practices workflow for my exome reads from tumor samples: I align with bwa mem, sort with samtools, mark duplicates and recalibrated bases with...
View ArticleRead Length Distribution in GATK-4
In GATK-3.8 I use -T ReadLengthDistribution but cannot find this function in GATK-4, is it still available?
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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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 to Prepare the normal.bam and tumor.bam files
Dear Sir, am new and currently trying to learn whole exome analysis of breast cancer samples using the GDC Bioinformatics Pipeline...
View ArticlePicard or GATK tools
Hi, some picard tools like MergeSamFiles were ported to GATK 4 beta. Now in the release version they are described as picard tools again. Even though they are part of the GATK and can be used as such....
View ArticleError in GATK4 MUTECT2
Hello I am using RNASeq somatic mutations calls, using GATK I got this error in somatic mutation using GATK4 Mutect:: BAM header sample names [S1]does not contain given tumor sample name S1 This is how...
View ArticleSomatic mutation calling - PON vs VCF
I have a dog tumor sample without matched normal. I know that it is recommended to have matched normal but for this specific data, it is not possible to get a matched normal sample. I see that in...
View ArticleGATK4 SplitNCigarReads RuntimeIOException: Attempt to add record to closed...
On a Linux cluster, I ran this command on a node (no job scheduler): ./gatk SplitNCigarReads -R /bigdisk/databases/genomes/human/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa -I 28_tumor.dedupped.bam...
View ArticleNo variants with GenotypeGVCFs on polyploid samples
Hello, I have two bam files with sequenced pooled individuals (16 and 20 individuals). I ran Haplotypecaller (gatk 3.8) by setting the ploidy option to 32 and 40 respectively for each of my samples....
View ArticleBQSR: Do I need to use selectVariants ?
I'am running BQSR in bootstrap fashion with recommended hard variant filtering as I have not a model organism . My question is do I need to first use selectVariants -ef (exclude filtered) or will those...
View ArticleChanging compression level in GATK 4.0.0.0
When running GATK 4.0.0.0, (in this case using Apply BQSR) the notice 11:36:10.430 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 1 appears. A bit of digging led me to the Python code in the...
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