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Exome sequencing - additional public data for variant calling
Hi, I'm new to exome sequencing, sorry if the questions have really obvious answers. My data set contains only 3 different samples from mother, father and daughter. So far I'm doing the standard thing...
View ArticleVariant with great support not called.
This SNP has 30 reads supporting it with most of them being mapq60 and good fred scores. using version 3.4-46-gbc02625 and my command was java -jar ~/GenomeAnalysisTK.jar -R...
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 ArticleWhy is HaplotypeCaller dropping half of my reads?
Hi I have been trying HaplotypeCaller to find SNPs and INDELS in viral read data (haploid) but am finding that it throws away around half of my reads and I don't understand why. A small proportion (8%)...
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 ArticleConfused by overlapping indels
Hi all, I'm currently confused about the snips called as shown below. If I am not mistaken, the first row shows gatk called an 34 bp insertion in sample 001 at position 3229753. It didn't call anything...
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 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 ArticleQuestion 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 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 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 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 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 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 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 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 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...
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...
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