Question: Best visual and interactive genotype matrix (VCF) exploration tool
1
gravatar for William
8 months ago by
William3.9k
Europe
William3.9k wrote:

What is currently the best visual and interactive genotype matrix exploration tool for large genotype matrixes, say the 1000 human genomes VCF?

So 100M plus variants, 1000+ samples, raw uncompressed VCF file size 1TB+.

One requirement is that it should do all kinds of filtering that bcftools (view) does:

http://www.htslib.org/doc/bcftools.html

But BCFTools does not meet the interactive and visual requirements. BCFTools is only interactive for small VCF files or when you use the tabix index for looking up a small region.

Another requirements if that the filtering is visual and interactive, like for example with a small genotype matrix in Excel. (I know bad idea but at least Excel interactive, visual and biologist friendly).

With interactive I mean that a filter criteria can be adjusted and you reall-time get back your updated genotype matrix. Even for complex queries were the full 100M+ variants for all 1000+ samples should be scanned the tool should be interactive.

Does something like this already exist? If so which tools? If not why not?

visual bcftools interactive vcf • 543 views
ADD COMMENTlink modified 7 months ago by willgilks210 • written 8 months ago by William3.9k
3
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum99k wrote:

People in my lab use KNIME to open/filter the VCFs : https://www.knime.org/

I'm currently playing with the following java-based tool : it displays 'part' of an indexed VCF file and you can filter the data using a javascript-based expression. you can try it as a webstart application at: http://redonlab.univ-nantes.fr/public_html/jnlp/jfxngs/ (requires java8/java webstart)

ADD COMMENTlink written 8 months ago by Pierre Lindenbaum99k

I tried installing on Ubuntu 16.04, and get home/wouter/bin/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/VcfStage.java:74: error: package javafx.beans.property does not exist, followed by many more of similar errors each pointing to a different package that doesn't exist.

Before that error the following was printed:

javac -version  
javac 1.8.0_121  
#compile  
javac -d /home/wouter/bin/jvarkit/_tmp-2.6.1 -g -classpath "lib/com/github/samtools/htsjdk/2.6.1/htsjdk-2.6.1.jar:lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:lib/gov/nih/nlm/ncbi/ngs-java/1.2.4/ngs-java-1.2.4.jar:lib/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar:lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar:lib/org/tukaani/xz/1.5/xz-1.5.jar:lib/org/xerial/snappy/snappy-java/1.0.3-rc3/snappy-java-1.0.3-rc3.jar:lib/commons-cli/commons-cli/1.3.1/commons-cli-1.3.1.jar:lib/org/slf4j/slf4j-api/1.7.13/slf4j-api-1.7.13.jar:lib/org/slf4j/slf4j-simple/1.7.13/slf4j-simple-1.7.13.jar" -sourcepath /home/wouter/bin/jvarkit/src/main/java:/home/wouter/bin/jvarkit/src/main/generated-sources/java /home/wouter/bin/jvarkit/src/main/generated-sources/java/com/github/lindenb/jvarkit/util/htsjdk/HtsjdkVersion.java /home/wouter/bin/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/JfxNgs.java

I'm not at all familiar with java-stuff so if you could point me in the right direction, that would be great :p

ADD REPLYlink modified 7 months ago • written 7 months ago by WouterDeCoster22k
1

@WouterDeCoster don't use openjdk (incomplete) but the official oracle java : http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

ADD REPLYlink modified 7 months ago • written 7 months ago by Pierre Lindenbaum99k
1

Right, that did the trick ;-)
I'm going to play a bit with it, for sure looks great. Thanks!

ADD REPLYlink written 7 months ago by WouterDeCoster22k

thanks I'm still working on it, I'll happy to get any feedback :-)

ADD REPLYlink written 7 months ago by Pierre Lindenbaum99k
1

I was a bit confused what the 'main screen' "set location of all frames to" option would do, having been too quick in the manual. In hindsight it's clear, but I wouldn't have wondered about it if the text would have been something like "change genomic location of all frames to", with maybe an example "chr17:32232-32932" already entered. Or a gene name, it's not immediately obvious which input is expected.

ADD REPLYlink written 7 months ago by WouterDeCoster22k
2
gravatar for willgilks
7 months ago by
willgilks210
United Kingdom
willgilks210 wrote:

I've found the Integrated Genomics Viewer pretty good http://software.broadinstitute.org/software/igv/. It displays vcf files, with variants coloured by genotype and good zoom and scroll functions .. limited for very big files. Also you can view bam and gwas data with it.

enter image description here

ADD COMMENTlink written 7 months ago by willgilks210
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