How to call SNP without confidence SNP ？
Hello! I have WGS data of 100 samples. There's few people work on my species,so I didn't find confidence SNP set to use. I follow the best-practices of GATK. And my question is how to get convinced SNP...
View Articlerules for max_alternate_alleles in HaplotypeCaller
Hi, I can't come to any clear conclusion how this parameter works. Help me, please. I worked on the same files with exact command but the max_alternate_alleles. In first command I put 1 for its...
View ArticleOpenMP multi-threaded AVX-accelerated native PairHMM in HaplotypeCaller not...
I'm unable to get a multithreaded instance of PairHMM to work in HaplotypeCaller with JDK 1.8 on my local machine (Intel 4770K 8-core i7 processor) running MacOS 10.12.6. I've tried both a pre-built...
View ArticleCore dump with HaplotypeCaller using GATK 3.7
I'm trying to run HaplotypeCaller on a single RNAseq BAM file, but I keep getting a core dump. I've tried allocating more memory (up to 150 GB RAM) and reverting to single-thread mode, but...
View Articledefault read filters in haplotypecaller in GATK 4.0.0.0
Hi, Are these still the read filters applied in GATK 4.0.0.0 haplotypecaller (gvcf mode)?- • HCMappingQualityFilter (Default 20) • MalformedReadFilter • BadCigarFilter • UnmappedReadFilter •...
View ArticlePloidy level in HaplotypeCaller in GATK 4.0
Hi, Thanks for the new version of GATK (GATK4.0). We have a pooling of 64 samples and the organism is diploid, we are using ploidy of 128 (64x2=128). earlier when I am using HaplotypeCaller for variant...
View ArticleSingle-Sample Genotyping: Different Workflow?
Hi, If I need to independently call and genotype a single sample, is there a different workflow or set of GATK tools and settings that I ought to use instead of using haplotypecaller to generate a GVCF...
View ArticleIs it useful to call LeftAlignIndels after IndelRealigner
Hi, In my pipeline to find variants in bacterial genome, I am first calling IndelRealigner and then calling variants using HaplotypeCaller. As left aligning of indels seems to be an important step,...
View ArticleIs GATK4 HaplotypeCaller in evaluation phase?
Hi GATK team, Congratulations on the release! I just found this public method in FireCloud that notes that HaplotypeCaller in GATK4 should not be used for production use yet since it is still in...
View ArticleForgot to add -ERC GVCF when using haplotypecaller
Hi, I have used the haplotypecaller to call the variants for my each sample without -ERC GVCF. Thus, I can not use the GenotypeGVCFs to merge them together. What should I do to resolve this problem?...
View ArticleConfusion in using gVCF mode
Hi I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems: 1- Should we run gVCF even when we have one WES sample? 2- I have 3 WES samples,...
View ArticleHaplotypeCaller and reads mapped to multiple locations
Dear GATK team, I've been trying to use GATK to call SNPs from RNA-Seq data mapped to a transcriptome assembly. I used Bowtie2 for the read mapping. I apologize if the information is already posted,...
View ArticleDetecting called Indels with low read support on both sides?
Hi, I am mapping chimpanzee samples to the human reference hg19. I mappend the samples using the standard protocol (BWA mem, remove duplicates, indel realigner) and called them with GATK 3.7 Haplotype...
View ArticleTesting Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)
Hi, I am a researcher from Chinese of Academy of Sciences. I am trying to test the FPGA implementation of the HaplotypeCaller (PairHMM) on GATK 3.8-0-ge9d806836, using a Intel Arria® 10 GX FPGA (Arria...
View ArticleGATK v4.0.1.1 HaplotypeCaller
I am using GATK v4.0.1.1 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem). The command I used; “gatk HaplotypeCaller –R Reference.fna –I...
View ArticleWGS+WES combined discovery/genotyping
Hi GATK team, Hope you had great holidays! We're analyzing small families where some individual have been sequenced by WES (HiSeqX) and others by WES (HiSeq4000). Could you please advise on the best...
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Missing or Inconsistent call between single-sample and multi-sample SNP calling
Dear all, I have generated a gVCF file using HaplotypeCaller (v3.7)and searched for a specific variant of interest which looks like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT N417 chr1 627033...
View ArticleHaplotypeCaller warnings DepthPerSampleHC
Hi I'm trying to do a multisample variant call using several bam files in the following cmd /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa...
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HaplotypeCaller may fail to detect variant with the same reads with a...
I have experienced a variant detection issue with confusion. The png file attached is the result of exact same NextSeq experiment but the read extraction range is different. NextSeq2_point.bam: bam is...
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Seeing multiple calls for the same position
Hello, I am running a trio through the best practices pipeline for 3.7 and finding an unexpected result. I am seeing some positions that are being called multiple times with different calls. First, as...
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