fastest way of getting total number of variants in VCF via picard?
What is the fastest way of getting the total number of variants in a VCF file? (using picard-tools-1.119, via SplitVcfs.jar.) So far the fastest way I could have done it was this: private static int...
View ArticleHelp for using GATK
I hava a question wish to get help from the developers: I am using GATK with two modles: 1, I just use the UnifiedGenotyper to call the variants from a prepared bam file, then I get a vcf file. (Call...
View ArticleIs it possible to make VariantAnnotator check REF and ALT fields?
Hi! So we use GATK a lot in our research, it works amazingly well most of the time, so first of all, thanks for creating it! We have this one problem that we were unable to solve on our own. Say we...
View ArticleSingle Sample VQSR
Hi all! I've got a questions concerning the VQSR. The situation is as follows: - I've got more than 100 Single Sample VCFs - Unfortunately I wont be able to re-call the VCFs - Merging the Files into a...
View ArticleReturn the entire VCF contents via picard?
Hi I would like to know how can I return the entire contents of a VCF file without having to know the chromosome/start/end parameters. The VCFFileReader class has a query method that can return parts...
View Articleinvariant calls not consistently included in Unififed Genotyper output
Hello! I am writing to seek your help on a curious result I received from running the Unified Genotyper. I ran Unified Genotyper to obtain all confident sites (both invariant and variant) on a suite of...
View ArticleEqual supported reads along with genotype of 0/1
Hello, I use HC to call variants, and there is a record like this: chr15 90172419 rs143394914 GGGGTGGGGGCTGTGGGCTGGGT G 88.77 ....
View ArticleIs it possible to get haplotype sequences for samples from a vcf SNP file and...
Hi, I would like to know if it is possible to get haplotype sequences for samples from a vcf SNP file and a reference sequence. The fact is that I took back from a paper a vcf file and a reference...
View ArticleGenotypeGVCFs
I was trying to do combine sets of vcf files for all my samples so that I have one single vcf output using this command option below java -d64 -Xmx48g -jar ${GATK}/GenomeAnalysisTK.jar \ -R ${REF} \ -T...
View ArticleLower GATK's HaplotypeCaller threshold for allele frequency as part of a...
Hi! As part of a variant calling pipeline i'm interested in lowering the threshold for allele frequency tolerance in GATK's HaplotypeCaller variant caller to 0.01 (1%), if possible. If not, is there...
View ArticleSome sites that are overlapped by a spanning deletion getting a REF call...
It appears that there are some cases in which an upstream site is heterozygous for a deletion, and a downstream site should be heterozygous for something like 1/2 (where 2 is the * allele), but GATK is...
View ArticleError when trying to fix the contigs order in the reference and vcf for...
I am trying to use a VCF containing snps variants to change the mouse reference (GRCm38- c57BL/6J) with BALB/cJ snps. After running this command: java -jar ~/programs/GenomeAnalysisTK.jar -T...
View ArticlePicard LiftoverVcf
I am having a problem with picard's LiftoverVcf. I am trying to Liftover hapmap files (downloaded plink files from hapmap and converted to vcf using plink) from ncbi36 to hg38. I was able to do this...
View ArticleEMIT_ALL_CONFIDENT_SITES option, omitting non-'LowQual' sites
Hi, I've run UnifiedGenotyper on a BAM file with both EMIT_ALL_SITES and EMIT_ALL_CONFIDENT_SITES. I've noticed some of the calls that have been omitted with the EMIT_ALL_SITES option seem to be of...
View ArticleNormalization of multi allelic polymorphism
Hi, I just read the article "Unified Representation of Genetic Variants" (A. Tan) They propose a way to normalized variants. As mention in this forum, GATK has a tools to normalized biallelic...
View ArticleAD in VCF doesn't match BAM
Hello, I'm using GATK to call variants in my RNA-Seq data. I'm noticing something strange, perhaps someone can help? For a number of sites the VCF is reporting things I cannot replicate from BAMs. How...
View ArticleIn a VCF file, when DP=0, why it stills give a Genotype?
I am dealing with my data using vcftools, in the generated vcf file, I found that when DP=0, why it stills give a Genotype, like 0/1 0/0 or something? I attached a pic, a screenshot from a vcf file....
View ArticleVCF file and allele frequency
Hello All, I am using I am using GATK RNA-seq variant pipeline for finding muttaion/vatiants on the list of gene given in teh follwoing command line java-1.7 -jar -Xincgc -Xmx1586M...
View ArticleHomo_sapiens_assembly19.kown_indels.vcf vs....
Have a long standing stable pipeline, which I need to tweak as can be explained and justified. What is the difference between the old file of known indels (from Mills paper(s)) -...
View Articleto combine multi-sample variants with tumor-normal comparison vcf files.
Dear all, When I combined multi-sample variants with tumor-normal comparison vcf files, following errors emerged. It is normal for triallelic variants in tumor. Could you please tell me how to fix the...
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