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Errors about contigs in BAM or VCF files not being properly ordered or sorted
This is not as common as the "wrong reference build" problem, but it still pops up every now and then: a collaborator gives you a BAM or VCF file that's derived from the correct reference, but for...
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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 Articlehow to build GATK 3.7 ?
Hi, professor, where I can download useful GATK 3.7 source code ? how to build that ? can you give me some detailed introductions ? thank you !
View Articlehow to build gatk?
I'm trying to build gatk from the source but I can't find any guides on this. I tried cloning the git: git clone git://github.com/broadgsa/gatk-protected.git then running "ant" from that directory....
View ArticleHow to input covariate table to GATK4-Alpha Print Reads
I'm trying to run PrintReads in GATK4-Alpha and apply the BaseRecalibrator covariates table. Using java -Xmx80G -jar $GATK PrintReads -R umd_3_1_reference_1000_bull_genomes.fa -I GA1442_dedup.bam -O...
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Problems interpreting Mutect2 output
Hello, I am calling variants with Mutect2 (default parameters) from bulk WGS Tumor/Normal pairs following Somatic SNV Best Practices, and in the VCF outputs I am finding a lot of variants like this...
View ArticleUnderstanding GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 and GT:DP:GQ:MIN_DP:PL...
Hi GATK team, I used the following command to create a per-sample GVCF: java -jar GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T HaplotypeCaller --genotyping_mode DISCOVERY --emitRefConfidence GVCF...
View ArticleMemory setting issue in CNV calling pipeline step 2: SVAltAlign
Hello, I failed in running CNV calling step 2: SVAltAlign, probably because of the memory setting issue. Even though the "-lsfMemLimit 128" is specified in the command, which is: "java -Xmx128g -cp...
View ArticleMutect2 output not match to real situation
Hello, I used Mutect2 to call variants on a pair of tumor and normal samples. One variant "PASS" the filter is shown below: 4 6956086 . C CTTTCTTGCT . PASS...
View ArticleWGS HC call intervals for GRCh37.p13
Hi Team, I saw in post #9394 that you provide calling interval files for WGS. Great idea! I found one in the bundle but only for hg38. Did I miss something similar for GRCh37.p13, or is this planned?...
View ArticleSelect SNP and reference monomorphic sites from a large callset
Dear all, Recently, I have called genotype using GenotypeGVCFs with --includeNonVariantSites. I want to pull out the sites with one allele or . in ALT column. I found the following command will also...
View ArticleInvalid command line: No tribble type was provided on the command line and...
Dear GATK support team, I have created g.vcf files from 2000 samples. Following GATK's best practices, I want to combine them in sets of 200 samples before proceeding with the joint genotyping. When...
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Reference Genome Components
Document is in BETA. It may be incomplete and/or inaccurate. Post suggestions to the Comments section. This document defines several components of a reference genome. We use the human GRCh38/hg38...
View ArticleShould reference sequence surrounding homopolymer warning site show a long...
Hi, I am using Variant Annotator to annotate my vcf. One of the annotations is Homopolymers run - I get several error messages like the one below regarding homopolymers. I have looked at the reference...
View Article--pcr_indel_model
Hi I have a question about s --pcr_indel_model. My library is PCR free library and will use HiSeqX for sequencing. Even though the library is PCR Free, but HiSeq X has clustering duplicate. In this...
View ArticleSelectively eliminating a set of chromosomes per sample in a multisample VCF
Hello, In my multisample VCF file, some samples have aneuploid chromosome numbers. For example, Sample1 might be 2N for chr1, chr2, and chr3. Sample2, however, might be 2N for chr1 and chr3, but 3N for...
View ArticleSTAR-2 pass mapping
I want to use STAR 2-pass alignment steps for SNP detection in RNAseq data: But I am getting very confused, I using STAR 2.5.3a version: I can understand the there 4 steps need to perform in STAR 2-...
View Articlemissed variant calling for amplicon-based sequencing data using HaplotypeCaller
Hi all, I am using GATK v3.7 HaplotypeCaller to genotype 2000 dbSNP variants, including SNPs and INDELs, from amplicon-based sequencing data. --alleles is applied in HC, however, nearly 100 SNPs can...
View ArticleQuestions about PublicPairedSingleSampleWf_170412.wdl
Hi there, I was following the tutorial (How to) Map and clean up short read sequence data efficiently when I discovered the link to the complete protocol in WDL. After having run several steps, I have...
View Articleoncotator cmd vs website result difference
Hi, I just installed the oncotator v1.9.1.0 using the virtualenv option. With this I am using the oncotator_v1_ds_Jan262014 database. When I run oncotator for about 20 mutations, I get different...
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