Variant calling with multiple individuals and libraries.
I have multiple individuals. Let's say they are S1 (Subject 1), S2 and S3. There are two Chip-seq libraries for each subject (AC, ME). So I have 6 libraries in total. S1_AC, S1_ME, S2_AC, S2_ME, S3_AC,...
View ArticleI get very different MQ values when using GVCF vs BP_RESOLUTION
Hello! I had a question about the difference between using HaplotypeCaller's --emitRefConfidence GVCF vs BP_RESOLUTION. Maybe the answer is obvious or in the forum somewhere already but I couldn't spot...
View ArticleBug with version 3.6 and jexl
I recently tried to use a GaTK command I previously used with GaTK 3.5, and I'm getting a jexl error. I don't understand why. I've updated to java 1.8.0_77 java -Xmx${MEM} -jar...
View Articledisabling duplicate read filter with Mutect 1.1.4
I would like to use -drf DuplicateRead with Mutect 1.1.4, but I get command not found for -drf. I guess this is because Mutect 1.1.4 runs with GATK v2.2-25-g2a68eab whereas the -drf option is available...
View ArticleWhy am I getting high GQ scores for doubtful calls?
Actually, there are several aspects to this. I am looking for de novos in trios and basically I have far too many, indicating incorrect calls with HaplotypeCaller. One example which highlights a number...
View ArticleHaplotype caller -L option
Hi, I am running GATK v 3.5 using -L on multiple chromsomes to create gVCFs. -L 1,2,4 does not work, individually -L 1 are working. Just wondering if this is expected behavior. if so, can you advise...
View ArticleMultiples samples filter with DP < 10
I am trying to call SNP from two different samples and after that filter SNPs based on DP > 10 in each sample. If at a locus, any one sample doesn't meet the requirement then remove the locus. It...
View ArticleValues for QD annotation not detected for ANY training variant in the input...
Hi, I looked at previous answers to this problem, but it doesn't seem to explain what is happening. I used haplotype caller on 45 exomes (output g.vcf files), then I did a joint genotyping using -T...
View ArticleOne plot error about CNVpipeline stage5
Hi, I met another error about GenomeStrip2.0 CNVdiscoveryPipeline, and it stopped at stage5. Some parts of the error log are as following, ERROR 09:59:48,040 FunctionEdge - Contents of...
View Articlesplitting multiple samples from the VCF file
Hi, I am working on removing some unwanted samples from a VCF file or splitting multiple samples from the the VCF file by using SelectVariants tool. For splitting multiple samples I did the following...
View ArticlePicard SortSam error Unrecognized tag type
I'm running several samples through a pipeline and using Picard 1.80 and Java version 1.7.0_51. Most of the samples are running fine but I got this error message for two of the samples:...
View ArticleRecommendation / best practices GVCF GQ bands
Dear GATK team, Do you have any recommendation or best practice guidelines on the GVCFGQBands setting? This used to be (gatk < 3.2) [0,5,20,60] but has been changed one block per GQ value in gatk...
View Article(howto) Test your GATK installation
Objective Test that the GATK is correctly installed, and that the supporting tools like Java are in your path. Prerequisites Basic familiarity with the command-line environment Understand what is a...
View ArticlePON in Mutect2
Hello, Is it possible to use a VCF generated by GATK Haplotype Caller, as input for the PON VCF into Mutect2? or is it required to generate the PON VCF with the Mutect2 caller? Thanks Severine
View Articlesample prepared from multiple flowcell and multiple lanes
Hi, I have multiple paired-end fastqs from a single biological sample that was prepared by three flowcells, two lanes each. In short, I have sample_flowcell1_lane1.R1.fastq.gz...
View ArticleQuantity and quality of SNPs
What can be probable reasons for getting very less SNPs in compare to other tools for non-model organism.
View ArticleHaplotype Caller output
Hello, After the data preparation steps, I run HaplotypeCaller on my analysis ready data (bam files). I give a list of ~60 SNPs in the vcf file, but very few of them (<10) appear in the output. I...
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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 ArticleCombineGVCF Error: Malformed VCF
Hi, I generated a GVCF per (human 30x whole genome sequencing) sample per chromosome using HaplotypeCaller, then I would like to combine the GVCFs using CombineGVCF. I got the following error for some...
View ArticleCould not run picard.jar SortVcf
Hi, When I ran this java -jar /hpf/tools/centos6/picard-tools/2.5.0/picard.jar SortVcf SD=genome.dict I=new.vcf o=Newdbsnp.vcf it shows: [rzeng@qlogin4 reference]$ [Sat Aug 06 18:02:21 EDT 2016]...
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