Clik here to view.
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 ArticleClik here to view.
Combine Variants on numerous vcf
Hi GATK team, Is there a way to use CombineVariants on multiple vcf files, without retyping the "-V A.vcf -V B.vcf -V C.vcf etc." for each and every vcf file? we usually have 50-100 vcfs to combine, so...
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 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 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...
View ArticleDoes GATK 4 support multiple bam files as input?
In the command line help message, it says --input,-I:String BAM/SAM/CRAM file containing reads This argument must be specified at least once. However, if we actually give multiple input files, it says...
View ArticleClik here to view.
Somatic copy number variant discovery (CNVs)
Purpose Identify somatic copy number variant (CNVs) in a case sample. Requires an appropriate Panel of Normals (PON). Reference Implementations Pipeline Summary Notes Github FireCloud Somatic CNV case...
View ArticleClik here to view.
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 sequencing machine when it estimates the accuracy of each...
View ArticleGATK runtime error (READ_MAX_LENGTH must be > 0 but got 0) with 1000g bam
Hi, I'm trying to build a pon with GATK 3.7-0 to use with mutect2. For that, I've downloaded 80 exome bam files from the 1000g project (GBR, TSI, IBS and CEU populations). For most of them, when I try...
View ArticleHow is "ALLOW_N_CIGAR_READS" implemented in GATK4?
I'm running ASEReadCounter from GATK4. In the GATK versions prior to 4, there is parameter "-U ALLOW_N_CIGAR_READS" which is necessary for processing RNA-Seq alignment. However -U is not available any...
View ArticleCould I run ASEReadCounter on homozygous SNPs?
The documentation of ASEReadCounter states that this tool is designed for heterozygous SNPs. However, could I still use it to calculate ref and alt allele read depth on hom-SNPs? My purpose is to check...
View Article*bam files with the same size (# of contigs) to merge?
Hi, I am trying to merge multiple (4 files data fom UCEs) *bam files using MergeSamFiles.jar. However, the script shows this message: Exception in thread "main"...
View ArticleClik here to view.
(How to) Call somatic mutations using GATK4 Mutect2
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions and read about updates in the Comments section. This tutorial aims to introduce researchers with considerations in somatic...
View ArticleRealignerTargetCreater: A USER ERROR has occurred: '-T' is not a valid command.
Hi, I was running GATK RealignerTargetCreater . I ran the same command before with another bam file and it ran fine. Both of the bam files were produced using BWA MEM, sorted, indexed, fixed mate...
View ArticleGATK4 resource bundle
Hi, I was wondering if you guys are planning to release a new resource bundle with full hg38 support (+patches)? Perhaps to celebrate the release of GATK4? Thanks M
View ArticleClik here to view.
(How to) Map reads to a reference with alternate contigs like GRCh38
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section and be sure to read about updates also within the Comments section. This exploratory tutorial...
View ArticleValues for QD annotation not detected for ANY training variant in the input...
Hi, I am running VariantRecalibrator on 2 WGS using the command: gatk VariantRecalibrator \ -R ./hg38/Homo_sapiens_assembly38.fasta \ -V combinedgVCF.g.vcf.gz \ --resource...
View ArticleBWA MEM is not working
Dear Folks I started learning sequencing using GATK howto tutorial https://software.broadinstitute.org/...le.php?id=8017 I ran command bwa index chr19_chr19_KI270866v1_alt.fasta and it generated 5...
View Article