Missing PS field in the VCF file produced by GenotypeGVCFs
Hello, I followed GATK best practices to produce a VCF file for 20 individuals. GATK version is 4.1.0.0. The BAM files were all verified by ValidateSamFile, no errors or warnings were detected....
View ArticleHow to add sample names in VCF?
I am using GATK best practices for germline SNPs and Indels 4.1.2.0. After mapping and recalibration, I run haplotypecaller in GVCF mode. I am combining all vcf files (output from haplotypecaller)...
View ArticleAre there issues with using reads coming from different technologies and...
Hello! We are analyzing a WGS data of 60 samples (6 groups, 10 samples/group) produced by HiSeq4000. The mean coverage per sample is 25x (lowest sample is 15x). Now we realized we need to sequence more...
View ArticleWhere can I find dbsnp_144.hg38.vcf.gz
I'm installing an application that uses files from the GATK resource bundle. I found all of the needed files at...
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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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...
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