HaplotypeCaller not generating DP field
I am using GATK 2.5, and am calling HaplotypeCaller as java -Xmx4g -jar GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T HaplotypeCaller -I sample.bam -o hap.vcf -L subset.bed -dt NONE -D...
View ArticleHaplotypeCaller on 2000 samples, feasible?
I have previously tested HaplotypeCaller (GATK 2.7) on 100 samples. It takes a long time to run compared to UnifiedGenotyper. Is it feasible to use HaplotypeCaller on 2000 samples? Can I make it run...
View ArticleHaplotypeCaller doesn't call true variants which are located on the outside...
Hi, I was running the haplotypeCaller for many samples, but some variants (validated as true positives by using other techniques) within these samples are not called by the haplotypeCaller. I saw in...
View ArticleReduceReads - No real operator (M|I|D|N) in CIGAR
Hi. When I reduce my BAM files with ReduceReads and then run HaplotypeCaller I get this warning: Ignoring SAM validation error: ERROR: Read name 1060, No real operator (M|I|D|N) in CIGAR Why is this?...
View ArticleHaplotypeCaller is slow
My variant calling seems very slow. What do you think? We have 10 BAM files, each about 2.5GB, covering a targetted region of about 15MB. I am using the HaplotypeCaller with 8 threads (-nct 8) and it...
View ArticleHaplotypeCaller sensitivity
Hi there, I compared HaplotypeCaller and UnifiedGenotype of the latest version of GATK (2.7-4) on the same NA12878 trio. It seems HC missed some true variants (specifically, 7 out of the 49...
View ArticleHaplotypeCaller produces incomplete output
I am using GATK 2.7.2. I am working on the Best practices of GATK. I have followed all the steps as mentioned for Best practices. All the .vcf files that are needed as input are downloaded from ftp...
View ArticleRelease notes for GATK version 2.8
GATK 2.8 was released on December 6, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history Note that this release...
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(BP2.0) Variant Discovery
This article is part of the Best Practices workflow document. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow. Once you've pre-processed your data according to our...
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(BP2.1) Calling Variants with HaplotypeCaller
This article is part of the Best Practices workflow documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow. Many variant callers specialize in either SNPs or...
View ArticleHaplotypeCaller calling as heterozygotes incorrectly
I am finding that HaplotypeCaller is calling heterozygotes when there is no evidence when you look in IGV. Is this still a known problem? I am using version 2.8-1-g932cd3a. Attached are two screen...
View Articlehaplotypecaller and recalibration relations when workin on rough reference...
Hi, Would it matter a lot to do recalibration before usage of hc? If yes, it's worth to do realignment before recalibration to reduce no of snv's, I guess. I'm searching for variants in one of not too...
View ArticleHaplotypeCaller throws ERROR: Stack trace on generating raw variants VCF
Hello, This is in regards to a small exome capture experiment that I'd recently talked about here:...
View ArticleGATK and Berkeley Lab Checkpoint/Restart, RUNTIME ERROR, runtime must be >= 0
I am using GATK 2.7 HC with Berkeley Lab Checkpoint/Restart (BLCR). After I checkpoint and restart my job on the cluster I get the stdout and stderr shown below. I think I got it, because the restart...
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 ArticleHaplotypeCaller for calling 454 Indel
hi, Can i use HaplotypeCaller to call the 454 indel? Can anyone share his/her idea?thanks. Best, J
View ArticleHaplotypeCaller for 454
hi , Can i use HaplotypeCaller for 454 bams' SNPs and indel calling ? can anyone help to enlighten please..thanks very much :) Best J
View ArticleIs this expected that HaplotypCaller identified 40% more variants by 2.2.5...
Hi GATK team, I recently downloaded GATK2.2.5 and re-analyzed a small part of my data which was analyzed by2.1.8 pipeline previously, following the same parameters. However I found the new pipeline...
View Articlehow to run VQSR for individually called samples for rare variant discovery
We are running GATK HaplotypeCaller on ~50 whole exome samples. We are interested in rare variants - so we ran GATK in single sample mode instead of multi sample as you recommend, however we would like...
View ArticleHet calls from HaplotypeCaller with no ALT reads
Hi With HaplotypeCaller,Version=2.8-1-g932cd3a In the raw VCF we are seeing instances of GT:AD:DP:GQ:PL 0/1:22,0:22:53:53,0,2067 A HET call (0/1) but there are no ALT reads (22,0) Some Questions to...
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