SelectVariants - java.lang.IllegalStateException: Allele in genotype not in...
Hi everyone, I'm trying to select variants with SelectVariants but for some reason it stops saying that Allele in genotype CT* not in the variant context [CT*, C]. I tryied to find a CT* in the VCF...
View Articleunderstand HaplotypeCaller output vcf format
Hi there, I am using GATK4.1.0.0 version on germline pair-end illumina WGS data with following command: ``` gatk4.1.0.0 --java-options '-Xmx5G' HaplotypeCaller -R...
View ArticleProblem with a BED file and the flag -alleles (HaplotypeCaller)
I'm trying to pass the flag -gt_mode GENOTYPE_GIVEN_ALLELES by giving a list of SNP in a BED file. This BED file has 4 columns (chromosome, initial position, final position, allele, allele). However...
View ArticleSelectVariants by sample names file
I need to subset a list of samples from a large vcf.gz file. The sample names was saved in a plain txt file, each name in a row. I used -RF -sf my.sample.names.txt but kept getting error. Any...
View ArticleGATK4: RMSMappingQuality results differ between v4.0.0.0 and v4.1.1.0
Good morning everybody and thanks in advance for your advices and your help. I checked for this problem before submitting this question. I hope this is not a double. We are working with whole genome...
View Articlewhy variant callers's (GATK3.8 and GATK 4.0) results are different ?
hello, i am beginner . i used two different tools to analyze my data but i got the two different why ?
View ArticleGenimicDBImport too slow!!!
Dear all, I'm runnig GenomicDBImport for 30 samples. It takes soo much time and after 3 days job killed for walltime exceeded limit. I want to ask you If there is a way to let it become faster. I...
View ArticleThe bamout file results are inconsistent with the VCF file results
Hi, I use GATK4 were analyzed, and found that took place on a site of "bamout" file multiple mutations, respectively from G mutation is T, the number of reads supported mutation is 14, and from G...
View ArticleHaplotypeCaller output modes EMIT_ALL_CONFIDENT_SITES and EMIT_ALL_SITES not...
Dear GATK-Team, First of all, thank you for your great support and constant development of GATK! I was very pleased to see that the output mode options EMIT_ALL_CONFIDENT_SITES and EMIT_ALL_SITES were...
View ArticleUsing GATK SelectVariants to filter based on calculated allele frequency
Many of the variant callers I use, such as Pindel, do not include the AF or allele frequency value in the vcf output. However I still need to filter the vcf based on the allele frequencies of the Tumor...
View ArticleHow to select samples that are polymorphic on a specific locus from a joint...
Hi, I am trying to select the samples that are polymorphic on a specific locus from a joint genotyped vcf file using SelectVariants tool and JEXL expressions with no success. The command I am trying to...
View ArticleNot understand the value in VCF file
Hi, I am sure if is right to ask the question here. I got the vcf file and need some help to understand the meaning. In the last two columns, there are some rows like: GT:CNADJ 0|1:2, I know 0|1...
View ArticleHow to get a smaller list of deNovo SNPs between 3 genotype
Hello. I am currently working on maize whole genome dataset and I have 3 samples- WT, MT and B73. I obtained the VCF files for all 3 datasets using the haplotype caller. However, the list of SNPs that...
View ArticleASEReadCounter not accepting VCF file as input
I'm trying to run ASEReadCounter, but it's not accepting a VCF file as input. I'm getting the following error: ##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command...
View ArticleMutect2 - java.lang.IllegalArgumentException: Cannot construct fragment from...
Hi, trying the latest version of Mutect2 4.1.4.0 java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false...
View Articlenon-reference allele didn't be called into vcf by HC
Hi GATK team I ran HC joint calling and found out that some non-reference alleles didn't appear in the vcf. Here are how these sites looks like: Most of these allele have VAF =1 and reside on the...
View ArticleHow to diagnose missing MQRankSum annotations (when BaseQRankSum is available)
We wish to discover short variants in a cohort of 60 plant whole-genome-samples. We're blocked on VariantRecalibrator. We have a VCF truth set (aka resource) of SNPs which has been computed beforehand...
View ArticleExtracting MQ and QUAL values for invariant sites in VCF files
I'm having problems getting mapping quality (MQ) values and PHRED called site quality scores (QUAL) for invariant sites in the VCF files generated by GATK, even when I specify that all sites should be...
View ArticleHow to identify duplicated genes in VCF file obtained after GATK pipeline?
I am working to find which gene type is more duplicated. I had mapped and annotated my VCF file by GATK pipeline. Please guide me how to proceed now.
View ArticleGT and AD
if my vcf indicates the GT is 1/1 and the AD=14,4: what does the 14,4 indicate? 14 reads of the ALT and 4 that were not???? or something else thank you
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