GATK 3 to GATK 4 and BQSR
Hello, I am trying to modify my exome pipelines to integrate GATK4. For the recalibration, I used with GATK 3 two round of BaseRecalibrator and used the recalibration table in happlotype caller with...
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Off-label workflow to simply call differences in two samples
Given my years as a biochemist, if given two samples to compare, my first impulse is to want to know what are the functional differences, i.e. differences in proteins expressed between the two...
View ArticleAbout the result of CNVDiscoveryPipeline
@bhandsaker This is the CNV result of my test: gs_cnv.genotypes.vcf.gz # But I have some doubt: 1. How can I select the CNV which belong to my test sample (there are so many background population)...
View ArticleFinish Running Svreprocess and Svdiscovery no result in xxxx.discovery.vcf.gz
When I finished Svreprocess, I check the output in xxxx.discovery.vcf.gz,there is nothing under the header ##fileformat=VCFv4.2 ##ALT=<ID=DEL,Description="Deletion">...
View ArticleInformation about the result of CNVDiscoveryPipeline
@bhandsaker hi Bob,I got the result of CNVDiscoveryPipeline In the vcf file: SVTYPE=CNV,How could I known this CNV is belong to DEL or Dup? and if it is Dup,how many times the CNV repeat? and what are...
View ArticleInvalid or corrupt jarfile
When I run ./gatk --help it seems to be working fine. However, running anything else such as ./gatk --list produces an error: Error: Invalid or corrupt jarfile...
View ArticleGATK for long reads like PacBio and Oxford Nanopore
Hi, I am aware that GATK is developed and used keeping illumina short reads in mind and it is also advised not to use them for calling calling variants using long reads. Just from a curiosity sake, on...
View ArticleInterpreting alt_allele_in_normal filter in Mutect2
Hi- If I understand correctly Mutect2, the alt_allele_in_normal flag is assigned when variant reads in the normal exceed the --max_alt_alleles_in_normal_count setting (which has default=1). I wonder if...
View ArticleVariantRecalibrator - no data found
I just updated to the latest nightly and got the same error: INFO 12:03:16,652 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00258 INFO 12:03:23,474...
View ArticleWhich version of Spark works well with the current GATK 4.0?
Hi, I am interested in using GATK4.0 with Spark on my PC. From previous posts I noticed that there is compatibility issue (errors) of GATK4 with the latest version of Spark (2.1 or 2.2 if I am...
View ArticleMutect 2 B38 germline resource
Hi, Congratulations on GATK 4.0! I'm looking at the instructions for Mutect2 where it suggests using a germline resource "--germline-resource af-only-gnomad.vcf.gz". Do you have a version of this for...
View ArticleMutect2 resources guide
A new tutorial for somatic calling We have a new tutorial, Tutorial#11136, that outlines how to call somatic short variants, i.e. SNVs and indels, with GATK4 Mutect2. The tutorial provides small...
View ArticlePICARD MarkDuplicates errors near the end of its process: tmp does not exist
Hi, I have a problem in that PICARD MarkDuplicates appears to error near the end of its process -- with a temp file not found error. This is running in a GATK pipeline on our cluster for WGS Best...
View ArticlePrintReads gets stuck
Hi GATK team! I am trying to do somatic variant calling with RNAseq data (following GATK best practices with paired-end Illumina reads). I have normals and tumors, and my pipeline runs from the fastq...
View ArticleThere is a bug in "CollectSequencingArtifactMetrics" in GATK 4.0
I am addressing WES data with GATK for mutation calling. I selected two samples to have a test. One is tumor sample, one is matched normal sample. I used bowtie2 to do the alignment (hg19). and then...
View ArticleInput files reference and features have incompatible contigs
Hi I am very new to GATK. i read the paper Curr Protoc Bioinformatics. ; 11(1110): 11.10.1–11.10.33. doi:10.1002/0471250953.bi1110s43 and best practices guide. i want to run whole exom analysis to find...
View Articlehi there,my script,there are many bugs
java -Xmx22g -jar /home/gatk/GenomeAnalysisTK.jar -T VariantFiltration -R /home/raw.fa -V /home/raw.vcf --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 ||...
View ArticleInstalling GATK4 via Conda
Hi there! I have a small problem, or a suggestion for improvement, related to the use of (Mini)conda and GATK4. I'm not entirely sure if this forum is a right place to ask this because I don't really...
View ArticleSingle cell snp-calling
Hi, I am dealing with some single cell data of breast cancer line. I have two questions: 1. I don't know if I need to make some changes when I do snp-calling on single cell data 2. Each sample (cell)...
View ArticleHaplotypeCaller with WARNNING DepthPerSampleHC
Hello, sorry for my bad English. While running GATK 4.0.1.1 Haplotypecaller with two or more bams together, this tool would send lots of lines of warning message about DepthPerSampleHC like follows:...
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