GQ
Hi, I found some strange rules from my VCF file. Most of snps which had high GQ, they also had high AF. However, why the snp which had low AF,they got low GQ? Does it make sense? Thanks for your help....
View ArticleFREEMIX and CHIPMIX in verifyBamID output
ran verifyBamID to check contamination and sample swapping for 2 projects. All data is from WES. bam file is from tumor sample, and germline mutations list as vcf file is from all blood samples. Ran it...
View ArticleLow Ti/Tv in Expanded Exome
Hello, I have a set of 72 Expanded Exomes, which after performing all steps from the Best Practices recomendations, I've done the VQSR. icav:mag$ java -Xmx6g -jar...
View ArticleVariantRecalibrator error
Hello, I am running the Variant Recalibrator command and running run into this error. is this because of multi threading or a different issue ? Many thanks, INFO 15:36:38,675 HelpFormatter -...
View Article-B:genotypes,vcf in ContEst
I do not have array data. I have matched samples of tumor and normal from each patient. I am trying to estimate contamination level of tumor sample. Can I find germline mutations from the matched...
View ArticleJexl commands; selecting multi or phased alleles
I am looking for a pathogenic variant in exome read data. To identify common inherited regions I would like to extract information from multiallelic sites or variants with phased data. Is there a way...
View ArticleNLOD and TLOD in MuTect2
Hi ! I'm trying to understand better the rationale of the algorithm behind MuTect2 (GATK3.6) . My question are based on your slides from a workshop (16th of September 2016). I just still cannot...
View ArticleGATK stalls on particular NCBI reference genome
Hi, I am upgrading my analysis pipeline from GATK 3.3-0 to 3.6-0 on a CentOS 6.x machine and came across a problem with GATK stalling at the following point in the output below (I know that it is not a...
View Articlepicard sortvcf
when I used GATK tool RealignerTargetCreator to realign my bam file to reference indel vcf files, it reports error that the two files have incompatible contigs. So I used picard ReorderSam and SortVcf...
View Articlewhy DP value in FORMAT (sample DP, I call SNVs in one sample) is higher than...
I use haplotypecaller for SNV calling in my whole exome capture sequencing project, but I found some abnormal result in the output of haplotypecaller (version GATK 3.6). It's abnormal to see the sample...
View Articlereadbackedphasing (HaplotypeCaller) outputs much more 0|1 then 1|0, why?
Hi! With the aim of phasing haplotype from SNPs of a single individual, I have used HaplotypeCaller which performes ReadBackedPhasing automatically (accuracy of SNP calling is beyond the question)....
View ArticleIncrease max allowed compute PLs for an allele
When running GenotypeGVCFs (v3.7), I get a small number of sites (<100) that are not called because of: DEBUG 13:35:31,518 ReferenceConfidenceVariantContextMerger - location chr21:44483184 has too...
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Base Quality Score Recalibration (BQSR)
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencer when it estimates the quality score of each base...
View ArticleStats in PhaseByTransmission Progress Log and output files differ- how to...
Hi, I have a question regarding PhaseByTransmission output files and the numbers as they appear in the log. I have a trio for which i did the following: called with HC3.5 in gVCF mode joint genotyped...
View ArticleHC step 2: Local re-assembly and haplotype determination
This document details the procedure used by HaplotypeCaller to re-assemble read data and determine candidate haplotypes as a prelude to variant calling. For more context information on how this fits...
View ArticleSpeed improvement of MuTect2
Hello, We are using MuTect2 for calling of somatic variants in RNAseq. So we only want to look at coding regions. I tried the -L flag for only coding regions but it was not improving the speed of...
View ArticleVariantsToVCF Error: Null alleles are not supported
Hi GATK team, I am trying to convert HapMap output files of TASSEL3 to VCF using the GATK VariantsToVCF tool. However, I am getting the error below. I used GATK v3.2-2-gec30cee. Do the "null genotypes"...
View ArticleConcurrentModificationException in GATK 3.7 GenotypeGVCFs
Hello, I updated to GATK 3.7 and am seeing the following error when running a pretty simple GenotypeGVCFs command. If you'd like bug reports elsewhere (github?) i'm happy to put these there instead....
View ArticleThe VCF file hava not fully output by using HaplotypeCaller
HI,GATK TEAM I have done the SNP and Indel calling about 21 samples by HaplotypeCaller, but I found there have some lines only have part of information in the VCFfile. The informations were cut from...
View ArticleTo run the programming "GenotypeGVCFs" too slow for my data, why??
my code: SAMPLE=" -V d_19_HC.gvcf -V d_F14_HC.gvcf -V d_F8_HC.gvcf -V d_M12_HC.gvcf -V d_M5_HC.gvcf -V d_X4_HC.gvcf -V d_X9_HC.gvcf " java -Xmx8g -jar $GATK -T GenotypeGVCFs -R $GENOME -nt 32 $SAMPLE...
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