A Gene Pattern Question
Hi, I was referred here but not sure if this is the right place to ask. Any comments will be appreciated. I am planning to run a Gene Pattern Module "CopyNumberInferencePipeline" on 240 tumor .CEL...
View ArticleEmpty VCF generated after using Mutect2
I tried running Mutect2 on tumor and matched-normal bam files for calling somatic mutations and after processing of 24hrs, I received an empty .vcf file along with index file (vcf.idx) of 27K. Here is...
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9 Takeaways to help you get started with GRCh38
We are starting official support of GRCh38, a reference genome with alternate contigs. In fact, going forward all of our new projects will use GRCh38. During this transition over the coming year, we...
View Articlepicard 2.6.0 ValidateSamFile produces an exception for BGZF file with invalid...
Hi, I ran out of disk space while running our mapping pipeline. When running picard's ValidateSamFile tool on one of the bam files, it produced the Exception below. I'm not sure this is a bug per se,...
View ArticleCan you consider updating /bundle/2.8/b37/human_g1k_v37_decoy.fasta.fai.gz?
Hi GATK team, I found that using 'human_g1k_v37_decoy.fasta.fai' with samtools1.2 gives a floating point exception after a look at the fai indexes of human_g1k_v37_decoy.fasta.fai and...
View ArticleLoss of Reads in HCMappingQualityFilter
Hi Thank you for your quick reply to previous query..... I have one another problem in HCMappingQualityFilter.... we have lost 35-40% reads in HCMappingQualityFilter....what could be the reason of...
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Can a biochemist with one Python course under her belt start running analyses...
Find out and learn some practical steps to cloud debugging. Specifically, I tested the alpha release of Google Genomics Pipelines API that uses the command-line. Down the road, we will post similarly...
View ArticleClipReads tool - only at end of read?
I would like to use the ClipReads tool to soft clip reads (in a bam file) that contain an exact match to a set of sequences (primer seqs). ClipReads should be able to do this, but the problem is with...
View Articlemissing FOXOG annotation for specific SNP variants in VCFs
Hi, We've run Mutect2 with OxoGReadCounts walker to obtain FOXOG annotation for somatic variants in VFCs. I know FOXOG annotation is only calculated for SNPs and when denominator (ALT_F1R2 + ALT_F2R1)...
View ArticleStar allele and weird genotype calling
Dear GATK team, I have an example of a deletion spanning another mutation resulting in a star allele and I need some help to understand the called genotypes. I have 3 individuals. Individual 1 has only...
View ArticleHaplotypecaller
Hi I'm using the Haplotypecaller 3.4 in my pipeline, and I've detected this Issue. Depth is 37, with such a huge quality and when looking at the last column I see a GT 1/1 suported by an AD of 0,0 and...
View ArticleGATK4-ApplyBQSR Missing ReadGroups in PublicPairedSingleSampleWf
He its me again, i have a Problem with the function ApplyBQSR which repace the PrintReads function. I run a modified local Version of PublicPairedSingleSampleWf, tested with the demo files from the...
View ArticleError on Running HaplotypeCaller
Hi Team I am trying to output all genotype calls on chr6 based on a given set of snps. I keep getting this message after the run finishes 0.1%. Is this error already solved in new version? or is this...
View ArticleAmplicon-Seq Edge Effects in MuTect2
Hi, I've been mostly successful in adapting MuTect2 for use with amplicon-based panels. The one issue I continue to run in to is at the edges of the regions that we are targeting. I've done a great...
View Articleconfusing error message ; complaint of missing header columns that aren't...
Hi, I pass to PadTargets an interval_list file, and it complains of missing columns....but the values are on the first line. Do you by chance notice anything wrong with what I'm doing? Note the...
View ArticleMuTect2 and Alternate Allele Calls
Hi there, We have a few calls in our dataset that are slightly confusing. We are getting a triallelic flag, which is expected, but only getting one alternate allele outputted to the VCF. The alternate...
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Variant Quality Score Recalibration (VQSR)
This document describes what Variant Quality Score Recalibration (VQSR) is designed to do, and outlines how it works under the hood. The first section is a high-level overview aimed at non-specialists....
View ArticleGATK HC joint call gives multiple lines for same variant
Hi, I was doing some QC and happen to see the following behavior that are not what i wanted/expected: chr4 151267927 . A C 43.77 PASS AC=50;AF=0.532;AN=94;DP=739 GT:AD:DP:GQ:PGT:PID:PL ... chr4...
View ArticleDream challenge PON
Hello, The Supplementary Data for the Dream challenge (http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3407.html) indicates that a panel of normals filter was used for the Broad's Mutect...
View ArticlePoor SNP calling results
Hello, I'm new to the world of bioinformatics so apologies if this is not as detailed as some of the other questions! I have performed the joint genotype haplotype caller on PCR free illumina...
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