Haplotype phasing somatic mutations from MuTect2 using read-backed phasing...
To whom it may concern, I have both normal and tumour sample and I also have the parental data (both mother and father) for the patient sample. I hope to first haplotype phase the SNP and INDELs from...
View Articlesingle-sample GVCF calling on DNAseq with allele-specific annotations
thanks a lot . I read the argument explanation, but due to my low ability, I still can not understand -G Standard -G AS_Standard why they need and when should I add they, thanks a lot
View Articlea chemotherapy site not appear in vcf and bam-out bam but apper in...
thanks a lot. I have a important question want to confirm with you. a very important chemotherapy site not appear in vcf and bam-out bam but apper in sorted.dedup.bam as the figure shows. the gayk.bam...
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HaplotypeCaller failed to detect variant.
I have experienced a variant detection issue in GATK4.1 and older(v3.6) in the following examples. I have two bam files: NA24385_partial.bam, NA24143_partial.bam. On the IGV's image above, both samples...
View ArticleDifference between HC and UG methods
When I compared the result of HaplotypeCaller and Unifiedgenotyper, I found some locus that only be calling variation by UG. However, the origin bam file and bamout file produced by reassembly both...
View ArticleCore dump when using GATK 3.7 haplotyper
I'm using gatk 3.7, java 1.8, human genome. For specific regions I'm using ploidy more than 2 due to specific aim of the question. /usr/bin/java -Xmx10G -jar...
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GATK 4.1 HaplotypeCaller detected the same variant in one technical...
Hi, I tried to use GATK 4.1 HaplotypeCaller to detect EGFR T790M variant in a few technical replicates. It turned out that HaplotypeCaller detected the same variant in one technical replicate, but...
View ArticleWhy I got chaotic results when I did snp calling for all-sites used by...
The version I used is gatk4.0.7.0. The shell script I used is: software/gatk-4.0.7.0/gatk --java-options "-Xmx4g" HaplotypeCaller -R NewChr.fasta -I split.bam -ERC BP_RESOLUTION -O ss.vcf I got the...
View Article[GATK4] combining g.vcf files for single sample on different intervals
I'm working with WGS using GATK 4.1.0 HaplotypeCaller to generate g.vcf file on many different non overlapping intervals. I'd like to have a single final g.vcf file for the sample. I'm trying to...
View ArticleJoint Genotyping
I ran GATKHaplotypeCaller without GVCF mode. I have got the correct output VCF file. I want to do the joint Genotyping for BSA QTLSeqr analysis. The GATK GenoType is only for gVCF. I cannot run this...
View ArticlePhysical Phasing Information HaplotypeCaller 4.1.0.0
Hi, I am looking to use HaplotypeCaller to call germline variants, and I am particularly interested in the orientation of these variants relative to one another (cis- or trans-). There seems to be...
View ArticleDifference in PL, DP values while running GATK 3.7 HaplotypeCaller on the...
We ran GATK 3.7 HaplotypeCaller upon a sample to get .gVCF file few months back. Recently we tested out the same sample with same parameters of GATK 3.7 HaplotypeCaller and found that there is...
View ArticleQuestions about calculating the genotype likelihoods
In this website, https://software.broadinstitute.org/gatk/documentation/article.php?id=4442, you showed the formula used to calculate PL. I can understand most of the formulas used here. But I can't...
View ArticleTwo validated variants missed by HaplotypeCaller using MIP data (amplicon...
Dear GATK, We are using MIPs (amplicon like) data to analyze the variants for certain genes. However, in two independent samples two validated variants were missed by the HaplotypeCaller. We were...
View ArticleCould you please let me know any tool, to concatenate the gvcf files? Or...
Could you please let me know any tool, to concatenate the gvcf files? Or there is any other solution to run the intermediate HaplotypeCaller in GVCF mode on parts of the chromosome to speed up the...
View ArticleNo variants found by HaplotypeCaller
I have human RNA-seq data: paired-end reads (2x150bp) aligned with STAR. I tried to run HaplotypeCaller with usual parameters: `gatk HaplotypeCaller -R GRCh38.primary_assembly.genome.fa -I...
View ArticleHow to create a Haplotype file from HaplotypeCaller
I am new to use GATK4. I would like to generate a Haplotype file (.bam or vcf file with haplotype information). I followed the Best Practice step till haplotypecaller. REF="refs/ucsc.hg19.fasta"...
View ArticleHaplotypeCaller bugs
Hi, I have tried to solve several issues which came up while trying to run the HaplotypeCaller. For this one, I didn't find anything on google and to be honest when pasting the error, google doesn't...
View ArticleWhy a variant site is listed in a GVCF run on a single sample, with no reads...
I have read couple documents on GVCF but still can't understand how it works. Just one example from the GVCF file I got from HaplotypeCaller from a single bam file with `-ERC GVCF` option: ``` chr22...
View ArticleHow do we know the stretch of variants that have been phased using haplotype...
I am using the following command to run haplotype caller /opt/apps/gatk/4.2.1/gatk HaplotypeCaller --dbsnp /home/dhwani.dholakia/archive/files_required_for_exome_analysis/dbsnp/GRCH37.p17_refseq.vcf -R...
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