ploidy level in HaplotypeCaller and GenotypeGVCFs
Hello, I am trying to make SNP calling of chloroplast DNA reads from 85 samples, using GATK v4.0. First, I used HaplotypeCaller to produce individual GVCF with the default ploidy setting. Making joint...
View ArticlePE mates are lost while downsampling with -dfrac?
Hi GATK team and users, I am using PrintReads with -dfrac option to simulate different depths of coverage. The original data contains WGS, PE reads (from GATK's Bundle bam, PrintReads with -L 20,...
View ArticleIndelRealignment step: Lost of reads?
I'm using IndelRealigner tool on my BAM file and then counting the number of reads in the BAM file using samtools stats and it turns out that in my input BAM I have 167170574 reads mapped while in the...
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 ArticleTroubleshooting: ERROR - variant files have inconsistent references for the...
Greetings, I am hoping to get some help troubleshooting a frustrating error I am having trying to genotype a large set of data. The source data is nearly 12000 WES samples, which were sequenced by a...
View ArticleDid GATK 4 break taking files containing lists of files from command line?
In GATK 3 I used to be able to provide the list of input files to GATK as a file containing a list of files rather than repeating the command line argument. Now with GATK 4 I get the error message:...
View Article# in file names converted to %23 resulting in file not found
Whilst I was trying to run CombineGVCFs 4.0.0 I got a very strange error, file not found for a file I knew existed. Looking into the backtrace it looks like somehow a # is getting mistakenly URL...
View ArticleReadBacked phasing vs Trio phasing?
I think I understand the technical difference. But in terms of phasing quality, how does one compare to the another? Are there any publications/reports/blog posts comparing the two? Is there some...
View ArticlePanel of Normals (PON)
A Panel of Normal or PON is a type of resource used in somatic variant analysis. Depending on the type of variant you're looking for, the PON will be generated differently. What all PONs have in common...
View ArticleHaplotypeCaller Reference Confidence Model (GVCF mode)
This document describes the reference confidence model applied by HaplotypeCaller to generate a per-sample GVCF, invoked by -ERC GVCF or -ERC BP_RESOLUTION. As explained here, HaplotypeCaller works by...
View ArticleConcatenating GVCF files in GATK4
Hello, I am currently running 60 whole genome sequences broken up into a number of non-overlapping intervals through HaplotypeCaller in GATK4. After I have created the GVCF files what is the best...
View ArticleHow is a haplotype called by HaplotypeCaller across the genome with RADseq data?
Hi, I had a question about how is a haplotype called by HaplotypeCaller across the genome with reduced representation sequencing data. I have ddRADseq data from a diploid organism and I used...
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 ArticleHow to Prepare the normal.bam and tumor.bam files
Dear Sir, am new and currently trying to learn whole exome analysis of breast cancer samples using the GDC Bioinformatics Pipeline...
View ArticleCurrent status of GATK4 GermlineCNVCaller tools and best practices.
Hi, I would like to try out GATK4 for discovering or genotyping germline CNV's in a cohort of few hundred whole genome sequenced samples. I work with non-human species data, but the genome sizes are...
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 ArticleNo variants with GenotypeGVCFs on polyploid samples
Hello, I have two bam files with sequenced pooled individuals (16 and 20 individuals). I ran Haplotypecaller (gatk 3.8) by setting the ploidy option to 32 and 40 respectively for each of my samples....
View ArticleAF in vcf files
There is some inconsistency in the community on how to calculate the AF (allele frequency) value in vcf files. GATK calculates a hypothetical value (0, 0.5 or 1 for normal diploid organisms). Other...
View Articletrio pipeline
Dear friends I am analyzing a trio I have followed the pipeline described in van der Auwera et al. 2013 on each person individually up to HaplotypeCaller and VariantRecalibrator is there a pipeline I...
View ArticleUndefined variable VariantFiltration
Hello I am filtering SNPs and indels for single sample targeted resequencing dataset. My command is: my $bigfilter_snps="-filter \"QUAL<80.0\" -filterName vm_QUAL -filter \"DP<20\" -filterName...
View Article