jvarkit
VcfGnomadPext
Peek annotations from gnomadpext
Usage
Usage: vcfgnomadpext [options] Files
Options:
--bcf-output
If this program writes a VCF to a file, The format is first guessed from
the file suffix. Otherwise, force BCF output. The current supported BCF
version is : 2.1 which is not compatible with bcftools/htslib (last
checked 2019-11-15)
Default: false
--bufferSize
When we're looking for variant in Gnomad, load the variants for 'N'
bases instead of doing a random access for each variant. A distance
specified as a positive integer.Commas are removed. The following
suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
Default: 10000
* -d, --database, --pext
Pext file. tab delimited :(chrom\tpos\tref\talt\ttx_annotation). Bgziped
and indexed with tabix.
-filtered, --filtered
Skip Filtered User Variants
Default: false
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --out
Output file. Optional . Default: stdout
-T, --tissues
Restrict to those tissues.
Default: []
--version
print version and exit
Keywords
- vcf
- annotation
- gnomad
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfgnomadpext
The java jar file will be installed in the dist directory.
Creation Date
20190220
Source code
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite vcfgnomadpext ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Context
https://www.biorxiv.org/content/10.1101/554444v1
“Transcript expression-aware annotation improves rare variant discovery and interpretation” Here, we develop a transcript-level annotation metric, the proportion expressed across transcripts (pext), which summarizes isoform quantifications for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression project (GTEx) and show that it clearly differentiates between weakly and highly evolutionarily conserved exons, a proxy for functional importance.
Example
# bgzip if needed and index the database with tabix
$ bgzip data.tsv
$ tabix -f -b 2 -e 2 -s 1 -c 'c' data.tsv.gz
# annotate
$ java -jar dist/vcfgnomadpext.jar -d data.tsv.gz input.vcf.gz
(...)
1 135803 . C G . . AC=8;AF=0.500;AN=16;DP=113;GNOMAD_PEXT=ensg:ENSG00000237683|csq:splice_acceptor_variant|symbol:AL627309.1|lof:LC|lof_flag:NON_CAN_SPLICE|Spleen:1.0|Brain_FrontalCortex_BA9_:1.0|SmallIntestine_TerminalIleum:1.0|Skin_SunExposed_Lowerleg_:1.0|Artery_Coronary:1.0|Brain_Hippocampus:1.0|Esophagus_Muscularis:1.0|Brain_Nucleusaccumbens_basalganglia_:1.0|Artery_Tibial:1.0|Brain_Hypothalamus:1.0|Adipose_Visceral_Omentum_:1.0|Nerve_Tibial:1.0|Brain_CerebellarHemisphere:1.0|Breast_MammaryTissue:1.0|Liver:1.0|Skin_NotSunExposed_Suprapubic_:1.0|AdrenalGland:1.0|Pancreas:1.0|Lung:1.0|Pituitary:1.0|Muscle_Skeletal:1.0|Colon_Transverse:1.0|Artery_Aorta:1.0|Heart_AtrialAppendage:1.0|Adipose_Subcutaneous:1.0|Esophagus_Mucosa:1.0|Heart_LeftVentricle:1.0|Brain_Cerebellum:1.0|Brain_Cortex:1.0|Thyroid:1.0|Stomach:1.0|WholeBlood:1.0|Brain_Anteriorcingulatecortex_BA24_:1.0|Brain_Putamen_basalganglia_:1.0|Brain_Caudate_basalganglia_:1.0|Colon_Sigmoid:1.0|Esophagus_GastroesophagealJunction:1.0|Brain_Amygdala:1.0|mean_proportion:1.0 GT:DP 1/10/0:39 1/1 1/0:25 0/0:11 1/0 0/1:38 0/1
1 135804 . G A . . AC=6;AF=0.375;AN=16;DP=82;GNOMAD_PEXT=ensg:ENSG00000237683|csq:splice_acceptor_variant|symbol:AL627309.1|lof:LC|lof_flag:NON_CAN_SPLICE|Spleen:1.0|Brain_FrontalCortex_BA9_:1.0|SmallIntestine_TerminalIleum:1.0|Skin_SunExposed_Lowerleg_:1.0|Artery_Coronary:1.0|Brain_Hippocampus:1.0|Esophagus_Muscularis:1.0|Brain_Nucleusaccumbens_basalganglia_:1.0|Artery_Tibial:1.0|Brain_Hypothalamus:1.0|Adipose_Visceral_Omentum_:1.0|Nerve_Tibial:1.0|Brain_CerebellarHemisphere:1.0|Breast_MammaryTissue:1.0|Liver:1.0|Skin_NotSunExposed_Suprapubic_:1.0|AdrenalGland:1.0|Pancreas:1.0|Lung:1.0|Pituitary:1.0|Muscle_Skeletal:1.0|Colon_Transverse:1.0|Artery_Aorta:1.0|Heart_AtrialAppendage:1.0|Adipose_Subcutaneous:1.0|Esophagus_Mucosa:1.0|Heart_LeftVentricle:1.0|Brain_Cerebellum:1.0|Brain_Cortex:1.0|Thyroid:1.0|Stomach:1.0|WholeBlood:1.0|Brain_Anteriorcingulatecortex_BA24_:1.0|Brain_Putamen_basalganglia_:1.0|Brain_Caudate_basalganglia_:1.0|Colon_Sigmoid:1.0|Esophagus_GastroesophagealJunction:1.0|Brain_Amygdala:1.0|mean_proportion:1.0 GT:DP 0/00/0 0/1:15 0/0:5 1/1:15 0/1:17 0/0:8 1/1:22
1 137619 . G A . . AC=7;AF=0.438;AN=16;DP=193;GNOMAD_PEXT=ensg:ENSG00000237683|csq:splice_donor_variant|symbol:AL627309.1|lof:LC|lof_flag:NON_CAN_SPLICE|Spleen:1.0|Brain_FrontalCortex_BA9_:1.0|SmallIntestine_TerminalIleum:1.0|Skin_SunExposed_Lowerleg_:1.0|Artery_Coronary:1.0|Brain_Hippocampus:1.0|Esophagus_Muscularis:1.0|Brain_Nucleusaccumbens_basalganglia_:1.0|Artery_Tibial:1.0|Brain_Hypothalamus:1.0|Adipose_Visceral_Omentum_:1.0|Nerve_Tibial:1.0|Brain_CerebellarHemisphere:1.0|Breast_MammaryTissue:1.0|Liver:1.0|Skin_NotSunExposed_Suprapubic_:1.0|AdrenalGland:1.0|Pancreas:1.0|Lung:1.0|Pituitary:1.0|Muscle_Skeletal:1.0|Colon_Transverse:1.0|Artery_Aorta:1.0|Heart_AtrialAppendage:1.0|Adipose_Subcutaneous:1.0|Esophagus_Mucosa:1.0|Heart_LeftVentricle:1.0|Brain_Cerebellum:1.0|Brain_Cortex:1.0|Thyroid:1.0|Stomach:1.0|WholeBlood:1.0|Brain_Anteriorcingulatecortex_BA24_:1.0|Brain_Putamen_basalganglia_:1.0|Brain_Caudate_basalganglia_:1.0|Colon_Sigmoid:1.0|Esophagus_GastroesophagealJunction:1.0|Brain_Amygdala:1.0|mean_proportion:1.0 GT:DP 0/1:25 0/1:10 0/1:46 0/0:32 0/0 1/0 1/1:31 0/1:49