No output file from Picard's MarkDuplicates
Hi, I'm working on a pipeline which takes a BAM file and produces a layout file for viewing in software the team uses. I'm working on unix command line and have Java/1.8.0_60 installed. I've integrated...
View ArticleWatch ##Thor: Ragnarok ##Full Movie Online
Watch ##Thor: Ragnarok Full Movie Online ? PLAY NOW ? http://bit.ly/2zupmzZ Thor: Ragnarok full movie free Thor: Ragnarok full movie online Thor: Ragnarok full movie 2017 Thor: Ragnarok full movie...
View ArticleRecommend way to compare GC bias across samples? Numerical values... no graphs
I'm trying to compare the gc bias of hundreds of sequenced genomes. What's the best way to do this numerically? SOFTWARE picard CollectGcBiasMetrics OUTPUTS: gc.summary_metrics.txt METRICS CLASS...
View ArticleHow to use multiple g.VCF files in GATK4.beta.1 GenotypeGVCFs?
Hi, I tried to use GenotypeGVCFs from GATK4.beta.1, but there seems to be still a bug with the --variants statement. At first I gave a list of my g.VCF files to it (ending .list as it worked in...
View Article!!..Husband can't make me happy wanna great Sex partner..!!
Sexually unhappy want great Sex partner who will see to my sexual needs. I could either suck you dry or you could fuck me in as many positions as you want.I just need a great pussy eater and...
View ArticleSpeed up HaplotypeCaller
Good morning, I am trying performed a HaplotypeCaller in pool samples. However, it's taking a very long time (more than 72h). I am using this command: java -XX:ParallelGCThreads=15 -jar...
View ArticleEmpty file with VariantsToVCF
Hi, I am trying to convert a dbSNP text file into a vcf file with the following command: java -jar GenomeAnalysisTK.jar -R canFam2_dog_genome.fa -T VariantsToVCF --variant:OLDDBSNP snp131.txt -o...
View ArticleClik here to view.
Calling variants on cohorts of samples using the HaplotypeCaller in GVCF mode
This document describes the new approach to joint variant discovery that is available in GATK versions 3.0 and above. For a more detailed discussion of why it's better to perform joint discovery, see...
View ArticleCollected FAQs about input files for sequence read data (BAM/CRAM)
1. What file formats do you support for sequence data input? The GATK supports the BAM format for reads, quality scores, alignments, and metadata (e.g. the lane of sequencing, center of origin, sample...
View Article(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
View ArticleLink to download Mutsig 2.0
I am not able to find link on the cgatools site as it only shows MutSigCV1.4 for download. Can someone please provide link to download MutSig2.0?
View ArticleCombineGVCF: java.lang.ClassCastException: java.lang.Integer cannot be cast...
Hi I'm trying to combine a bunch of gvcf's generated by bcbio-nextgen with GATK. However, when running the command I get the following error: INFO 09:32:20,508 GenomeAnalysisEngine - Preparing for...
View ArticleMissing parameter '-bqsr' in BaseRecalibrator of GATK version 4.beta.6
There is no parameter '-bqsr' in BaseRecalibrator of GATK version 4.beta.6 that could use to generate the 2nd recal table by include the 1st recal table.
View ArticleGenotypeGVCFs on BP_RESOLUTION mode and AD values
Hello, I have a question related to this one here by @bassu I've been working with HaplotypeCaller + GenotypeGVCFs on BP_RESOLUTION mode. I noticed recently that bcftools merge would refuse to merge...
View ArticleUsing Genome STRiP with data stored on a server
How would I go about running a genome set stored on a server when Genome Strip is on a local computer? Thank you.
View ArticleDifferent AS_QD values when genotyping a multi-allelic site alone or...
Hi, I have found that AS_QD values differ at multi-allelic sites when genotyping a multi-allelic site alone or when genotyping the whole chromosome on 4 batches of around 250 WGS samples using...
View ArticleVQSR on specific genomic region
Dear GATK Team, I have exome-data of many individuals (>2000) called with the HaplotypeCaller, but only of a specific set of genes from the genome. I would like to apply the VQSR-tool to recalibrate...
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 Articleproblem with RnaSeqMetrics in Picard CollectMultipleMetrics
When I try to run CollectMultipleMetrics with PROGRAM=RnaSeqMetrics and I= R= O= set to something I get : Exception in thread "main" java.lang.NullPointerException at...
View Article