Duplicate records after CalculateGenotypePosteriors
Hi, I follow this thread to execute results from a trio but I discover there are many duplicate records after CalculateGenotypePosteriors. Code brief describe here: java -Xmx16g -jar...
View ArticleGATK 3.8 PhaseByTransmission fails to update AC
Hi Using GATK 3.8 PhaseByTransmission the genotypes change for this call but does not update the AC (should be AC=3) which subsequently fails validation: 1 69270 . A G 252.64 MQ AC=4;AF=0.667...
View Articlejava training institute in chennai
how to choosing a java training institute according to best learning and I am in Chennai suggest me the best java training institute in Chennai
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Version highlights for GATK release 2.6
It's finally summer here in New England -- time for cave-dwelling developers to hit the beach and do the lobster dance (those of us who don't tan well anyway). We leave you with a new version of the...
View ArticlePicard or GATK tools
Hi, some picard tools like MergeSamFiles were ported to GATK 4 beta. Now in the release version they are described as picard tools again. Even though they are part of the GATK and can be used as such....
View ArticleCreateSequenceGroupingTSV
Hi! I copy and paste the code about CreateSequenceGroupingTSV and in this way I created a python file... When I'm going to run it I have the following error: :~/GATK4/IlluminaExomePairEnd/0.pipe$...
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Metrics say percent – Double-check those decimals – Fractions everywhere
Picard metrics that say 'percent' actually mean 'fraction'. Let's take metrics from MarkDuplicates as an example. Under PERCENT_DUPLICATION we see 0.134008. If we divide READ_PAIR_DUPLICATES by...
View ArticleDiagnoseTargets in GATK 4
Hi, if I understand this correctly there will be neither DepthOfCoverage nor DiagnoseTargets in GATK4: https://github.com/broadinstitute/gatk/pull/4094 How should I calculate the Coverage now? Will...
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Calling variants in RNAseq
Overview This document describes the details of the GATK Best Practices workflow for SNP and indel calling on RNAseq data. Please note that any command lines are only given as example of how the tools...
View Articlegatk3.8 vs gatk4 va gatk4spark ,the newer the slower!!
I use the gatk3.8 gatk4.0.0and gatkspark to test my data . I received a suprising result. gatk4 is slower than gatk3.8 ,and gatkspark is slower than them. The times are 17.3 vs 19.2 vs 24 min . The...
View ArticleWhat input files does the GATK accept / require?
All analyses done with the GATK typically involve several (though not necessarily all) of the following inputs: Reference genome sequence Sequencing reads Intervals of interest Reference-ordered data...
View ArticleHow is "ALLOW_N_CIGAR_READS" implemented in GATK4?
I'm running ASEReadCounter from GATK4. In the GATK versions prior to 4, there is parameter "-U ALLOW_N_CIGAR_READS" which is necessary for processing RNA-Seq alignment. However -U is not available any...
View ArticleCould I run ASEReadCounter on homozygous SNPs?
The document of ASEReadCounter states that this tool is designed for heterozygous SNPs. However, could I still use it to calculate ref and alt allele read depth on hom-SNPs? My purpose is to check...
View ArticleOpenMP multi-threaded AVX-accelerated native PairHMM in HaplotypeCaller not...
I'm unable to get a multithreaded instance of PairHMM to work in HaplotypeCaller with JDK 1.8 on my local machine (Intel 4770K 8-core i7 processor) running MacOS 10.12.6. I've tried both a pre-built...
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Deep learning in GATK4
By Sam Friedman, deep learning developer in GATK4 Over the past couple of weeks, there's been a lot of chatter online --and in the press!-- about the applicability of deep learning to variant calling....
View ArticleHow to includeing loci of non-variant in GenotypeGVCFs step with GATK4?
I called germline short variants using haplotype caller with GATK 4.0, and then I want to extracted the non-variants and variants ** into seperate files so I could filter them seperately. In the GATK...
View ArticleGATK 4.0.0 HaplotypeCaller -ERC GVCF error
Dear GATK Team, When I run haplotypecaller (GATK4.0.0) in -ERC GVCF mode with -variant_index_type LINEAR and -variant_index_parameter 128000, It's giving "A USER ERROR has occurred: v is not a...
View ArticleGATK runtime error: GenotypeGVCF
Hi, I was trying to use the GenotypeGVCFs tool on was data. I specify 8GB for heap (java -Xmx8g) and run the program but I get a runtime error. Is there something I should be doing differently? Also,...
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 ArticleStick to 3.5 or change to 4.0?
Hi, Until now we were using version 3.5 of the GATK toolkit in our group. Since we start with a new project now we think about moving to 4.0. However, staying with 3.5 would be convenient due to...
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