Problems in getting correct number of SNPs and INDELs in SelectVariant tool
Hi Everybody! I actually try to utilize a SelectVariant tool to separate my variants according to their types such as SNPs and INDELs in separate files respectively. After that i utilize the bcftools...
View ArticleEffect of LeftAlignAndTrimVariants with --splitMultiallelics tool
How does the LeftAlignAndTrimVariants with --splitMultiallelics tool affects the AC, AF, AN fields and also if multiple alleles are split then on what basis it splits the PL field which helps to...
View ArticleVQSR and VariantAnnotator on Samtools VCFs
Hi everyone! My goal is to run VQSR on VCFs generated with samtools mpileup. According to GATK best practices first i have to run VariantAnnotator on each of my VCFs in order to do that. here's the...
View ArticleX Chromosome gentyping
Now that GATK supports ploidy, how do people generate ChrX calls. My first guess is to have 2 separate genotyping runs, one for males with ploidy=1 and a second for females only with ploidy=2?
View ArticleExtracting consensus variants from a VCF with 27 RNA-seq samples from the...
Is there a tool, or recommended best practice for generating a consensus set of variants from multiple samples of the same genotype? In short I have 27 RNA libraries from different individuals and...
View ArticleVariantFiltration bug with filtering QualByDepth
Hi folks: My version info: /home/sn/software/java/bin/java -jar /home/sn/software/GATK/GenomeAnalysisTK.jar --version 3.8-0-ge9d806836 I've being using GATK HC -- GenotypeGVCFs -- VariantAnnotator --...
View ArticleX Chromosome gentyping
Now that GATK supports ploidy, how do people generate ChrX calls. My first guess is to have 2 separate genotyping runs, one for males with ploidy=1 and a second for females only with ploidy=2?
View ArticleThe function of -max_deletion_fraction argument
Hey people, Just wanted to clarify about the function of -max_deletion_fraction argument for UnifiedGenotyper tool. The documentation says: ""If the fraction of reads with deletions spanning a locus is...
View ArticleRG header SM field: pooling
The SAM standard and the GATK documentation both describe the SM field of the RG tag similarly, as containing the sample name, but when sequencing pools of samples, use the pool name instead of an...
View ArticleWhat is the best way to find denovo mutations in trios?
I have around 100 trios for which WES was done. My goal is to find denovo mutations in the child associated with each trios. So first I will do the following steps: 1 -Alignment to reference genome 2 -...
View Articleerror with GenotypeGVCFs
commands are: java -Xmx10g -jar $gatk -T HaplotypeCaller \ -R $refGenome \ --dbsnp $dbSNP \ -o s1.raw.var.g.vcf.gz \ -I s1.bam \ -pairHMM VECTOR_LOGLESS_CACHING \ --emitRefConfidence GVCF...
View ArticleHaplotypeCaller 4.beta.6 gVCF performance
Hi, ever since the 4.beta.4 release, I've noticed a significant increase in the memory requirements and execution time of HaplotypeCaller in gVCF mode. I tested the 4.beta.2 and 4.beta.6 version of...
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HaplotypeCaller missing SNP calls
Hi I am in the process of validating the HaplotypeCaller in gatk3.8, and it is missing some obvious SNPs in GRCh37. Playing around with various parameters I can make the variant being called or not....
View ArticleSNP/ INDEL calling in Bisulfite data
I have Bisulfite- treated sequence mapped using Bismark and Bowtie2 and I'd like to call SNPs and INDELs from it. I have used Bis-SNP to call SNPs but it doesn't call indels , can I use GATK to call...
View ArticledeTiN error
I run 7 samples with deTiN, 4 of 7 are not working and generate 3 different kinds of error. Since the other 3 samples works, I think it's not the formatting issue. The error messages are: 1.Cannot set...
View ArticleCNVDiscovery Troubleshooting
Hello, We are trying to use Genome Strip to process our data and seem to be encountering some errors when running CNVDiscovery. To assist with troubleshooting, a log file has been attached below....
View ArticlePICARD error
Hi I am running MarkDuplicate in PICARD, but I got an error. java -jar $PICARD MarkDuplicates \INPUT=aligned_reads.sam \OUTPUT=dedup_reads.bam \SO=coordinate ERROR: Unrecognized option: SO Any tips...
View ArticleVariantRecalibrator issue: Unable to create iterator for rod named input
Hi, I'm running into the following error: ERROR stack trace org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named input Any help or suggestions would...
View Article40 days to GATK 4.0
Release log, stardate holy crap it's December 1st. As we announced a little while back, GATK version 4.0 will be released into general availability on January 9, 2018. That means we have 40 days left,...
View Articlegatk 3.6 MIN_DP much lower then DP
I'm analysing a set of bacterial isolates, some which are (almost) identical to the reference, and some which are very different. Despite the fact that the identical isolates have good coverage (80x),...
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