Question of single calling and total calling
Hello: I met a question when I used the GATK pipeline. When I perform single calling for my Sample A & B, I get the results like: Sample A Chr01 2245 . A C,G 171.31 PASS ... GT:AD:DP:GQ:PL...
View Articledownsample_to_coverage in HaplotyperCaller
Hello, Here I have a question about downsample_to_coverage in HaplotypeCaller. I found -dcov cannot be used in HaplotypeCaller and I tried to change the values of parameters maxReadsInRegionPerSample...
View ArticleNaming SNPs..
Can a GATK tool automatically name detected variants, i.e. assign them a unique identifier within user-specified parameters?
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Missing variants with Haplotype Caller runs using multiple threads
Hi GATK team, First I'd like to thank you guys for the tools that you're making available for the community! The problem is that I have run my sample using Haplotype Caller and I faced some missing...
View Articlejava.lang.ArrayIndexOutOfBoundsException with HaplotypeCaller 3.2.2
Dear Sir/Madam, I am running HaplotypeCaller (GATK 3.2.2) and gets the error message below for some of the samples. I have seen this error posted before at the Forum and the recommendation has often...
View ArticleEmpty VCF file after runnin gHaplotypeCaller
Hi GATK team, I'm running HaplotypeCaller using the following command: -T HaplotypeCaller -R all.chrs.fasta -I filename.bam -o filename.vcf -stand_emit_conf 10 -stand_call_conf 20 -nct 8 -rf BadCigar...
View ArticleHaplotypeCaller does not call all variants
Hello. I am implementing my pipeline to Roche and I have a list of variants that are validated with Sanger. In my pipeline I am using HaplotypeCaller to call variants, but there are variants that are...
View ArticleHard filters for Haplotype Caller
Hi team, (this is really two questions) Do you have any recommendations for hard-filtering haplotypecaller-generated vcfs ? This was my previous filter for the unifiedgenotyper output"...
View ArticleHaplotypeCaller Error
Hi, when I try to run GATK HaplotypeCaller I always get the following error: > Non-monolithic file pointers must contain intervals from at most one contig unfortunately, I could not find the source...
View ArticleUnderstanding position of indels within VCF File [HaplotypeCaller]
Given the deletion-call of: I 308 . CT C 12492.73 What is the POS value (308) specifically denoting? Is it specifying the position at which the T would otherwise have been found in the reference if it...
View ArticleHaplotype caller: StrandAlleleCountsBySample (SAC) and multiallelic sites
I'm running haplotype caller (latest nightly build) with -A StrandAlleleCountsBySample parameter to get strand specific read counts (SAC). For variants with more than the default 6 maximal alt alleles...
View ArticleGATK HaplotypeCaller run
Hi, I am using HaplotypeCaller for variant calling on GATK version 3.2.2 on whole genome Illumina reads. I used the following command as per best practices with and without multithreading option...
View Article(howto) Call variants with HaplotypeCaller
Objective Call variants on a single genome with the HaplotypeCaller, producing a raw (unfiltered) VCF. Caveat This is meant only for single-sample analysis. To analyze multiple samples, see the Best...
View ArticleGATK HaplotypeCaller MIXED variants delins
Hello GATK team ! I am facing a problem that I am not exactly sure your caller can address and I would need your opinion on that. I use GATK last version (3.4.46) haplotypeCaller to call my variants...
View ArticlePhasing information for use in downstream tools
Hi, I know that HaplotypeCaller outputs physical phasing information in PG and PGT fields, so as not to confuse physical phasing with pedigree based methods, however if I wanted to use the physical...
View ArticleHaplotypeCaller and downsampling
What I have learned so far from other discussions about HaplotypeCaller: - read counts for positions with very high coverage are downsampled - this does not affect variant calling - this does affect DP...
View ArticleGenotypeGVCFs: running out of memory with >50 samples
Dear GATK, I used the HaplotypeCaller with "-dcov 500 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000" to produce 60 gvcf files, that worked fine. However,...
View ArticleHaplotypeCaller Memory 3.4.0
Hi, I am new to the HaplotypeCaller and have huge problems getting it to run ok. I have WGS re-sequencing bam files with ~30-60 coverage (bam files are >3GB in size). I am running these in ERC mode...
View ArticleHaplotype depends on kmer size - how to get just 2 haplos from haplotypeCaller
Hello, I am using HaplotypeCaller in order to get haplotype sequences from individual samples (several samples per species) for gene tree/species tree analysis. The reads are from an exome capture...
View ArticleGzipped gVCF files
Is there a way to use gzipped gVCFs files when using HaplotypeCaller and GenotypeGVCFs. If so how do you make the index files? I can't seem to get it to work. (I have searched the forum and can't seem...
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