I can't find anywhere what 'NEGATIVE_TRAIN_SITE' means in a VCF data after VQSR. (I have searched everywhere on GATK) I thought it meant that the variant is considered to be not on the truth site due to bad VQSLOD scores, and should be filtered out. However, in my VCF data, the VQSLOD score and whether 'NEGATIVE_TRAIN_SITE' is True or False does not correspond. What does this term stand for? Thanks :)
What does 'NEGATIVE_TRAIN_SITE' in VQSR mean?
158 Views Asked by JEJI At
0
There are 0 best solutions below
Related Questions in VCF-VARIANT-CALL-FORMAT
- Merging 2 VCF files using bcftools, however how should I update the fields according to 2 VCF files
- Separating alleles for 'bcftools merge' when ploidy >2
- How to write dataframe after converting vcf file to tidy dataframe with vcfR2tidy function in R
- Lack of consistency between snpEff annotation vcf file and the summary statitics generated
- BCFtools merge command collapsing non-identical variants to single record
- iterating on vcf file using cyvcf2
- Merging VCF Files and Expanding Metadata Efficiently
- base recalibrator --known-sites argument does not work
- How to convert the variant call format file (.vcf file) into a txt file with R?
- Outputting two different gsub results to two columns with AWK
- Extract summary statistic (beta, SE, EA, non-EA, EA frequency) from csv files (extracted from vcf) not working
- BCFtools fails to read regions inside nested while loop / for loop
- issue with FreeBayes in the multibam version
- Error when segregating sites of vcf using vcfR::seg.sites "Error in latag2n(x) : no method for coercing this S4 class to a vector"
- "File does not exist" error when running ensembl-vep with docker
Related Questions in GATK
- I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process
- Troubleshooting GATK Pipeline Error in AWS ParallelCluster Environment and Spark
- Parsing FORMAT and sample value fields from VCF file
- base recalibrator --known-sites argument does not work
- GATK4 is rejecting my RGSM when using AddOrReplaceReadgroups
- GATK Variant Filtration file Anopheles gambiae s.s
- New: Fatal error compiling: java.lang.NoClassDefFoundError: com/sun/tools/javac/main/OptionName: com.sun.tools.javac.main.OptionName
- BaseRecalibration by GATK
- How do I use this python function within the params section of my Snakemake rule?
- GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread
- Snakemake integrate the multiple command lines in a rule
- Snakemake first genotype of a vcf file as wildcard in output
- How to run ensembl-vep in conda
- Error running gatk HaplotypeCaller with allele specific annotations
- Snakemake: create multiple wildcards for the same argument
Trending Questions
- UIImageView Frame Doesn't Reflect Constraints
- Is it possible to use adb commands to click on a view by finding its ID?
- How to create a new web character symbol recognizable by html/javascript?
- Why isn't my CSS3 animation smooth in Google Chrome (but very smooth on other browsers)?
- Heap Gives Page Fault
- Connect ffmpeg to Visual Studio 2008
- Both Object- and ValueAnimator jumps when Duration is set above API LvL 24
- How to avoid default initialization of objects in std::vector?
- second argument of the command line arguments in a format other than char** argv or char* argv[]
- How to improve efficiency of algorithm which generates next lexicographic permutation?
- Navigating to the another actvity app getting crash in android
- How to read the particular message format in android and store in sqlite database?
- Resetting inventory status after order is cancelled
- Efficiently compute powers of X in SSE/AVX
- Insert into an external database using ajax and php : POST 500 (Internal Server Error)
Popular # Hahtags
Popular Questions
- How do I undo the most recent local commits in Git?
- How can I remove a specific item from an array in JavaScript?
- How do I delete a Git branch locally and remotely?
- Find all files containing a specific text (string) on Linux?
- How do I revert a Git repository to a previous commit?
- How do I create an HTML button that acts like a link?
- How do I check out a remote Git branch?
- How do I force "git pull" to overwrite local files?
- How do I list all files of a directory?
- How to check whether a string contains a substring in JavaScript?
- How do I redirect to another webpage?
- How can I iterate over rows in a Pandas DataFrame?
- How do I convert a String to an int in Java?
- Does Python have a string 'contains' substring method?
- How do I check if a string contains a specific word?