eiu bio excel tutorial for beginners on a mac

Eiu Bio Excel Tutorial For Beginners On A Download Appropriate Databases

The annotation procedure should take a few seconds in a typical modern computer.

The tutorial requires that you install conda in your personal computer, and it can be access here.

However, if you are already using a computing cluster and are already familiar with Linux, you do not need to follow this tutorial and can instead just read below.

Additionally, if the input is a VCF file, the program also generates a new output VCF file with the INFO field filled with annotation information.

You will see that the bin directory contains several Perl programs with.pl suffix.

Note that if you already added ANNOVAR path into your system executable path, then typing annotatevariation.pl would be okay instead of typing perl annotatevariation.pl ).

Eiu Bio Excel Tutorial For Beginners On A Download Appropriate Databases

The first a few commands download appropriate databases into the humandb directory.

The final command run TABLEANNOVAR, using ExAC version 0.3 (referred to as exac03) dbNFSP version 3.0a (referred to as dbnsfp30a), dbSNP version 147 with left-normalization (referred to as avsnp147) databases and remove all temporary files, and generates the output file called myanno.hg19multianno.txt.

Fields that does not have any annotation will be filled by.

Open the output file in Excel and see what it contains.

The expected output file that I generated can be downloaded here: ex1.hg19multianno.csv.

A screen shot of the first a few columns is shown below.

Each of the following columns corresponds on one of the protocol that user specified in the command line.

The Func.refGene, Gene.refGene, GeneDetail.refGene, ExonicFunc.refGene, AAChange.refGene columns contain various annotation on how the mutations affect gene structure.

The Xref.refGene column contains cross-reference for the gene; in this case, whether a known genetic disease is caused by defects in this gene (this information was supplied in the examplegenexref.txt file in the command line).

The other columns contains prediction scores for non-synonymous variants using several widely used tools, including SIFT scores, PolyPhen2 HDIV scores, PolyPhen2 HVAR scores, LRT scores, MutationTaster scores, MutationAssessor score, FATHMM scores, GERP scores, CADD scores, DANN scores, PhyloP scores and SiPhy scores and so on.

The -operation argument tells ANNOVAR which operations to use for each of the protocols: g means gene-based, gx means gene-based with cross-reference annotation (from -xref argument), r means region-based and f means filter-based.

If you do not provide a xref file, then the operation can be g only.

You will find details on what are generegionfilter-based annotations in the other web pages.

Sometimes, users want tab-delimited files rather than comma-delimited files.

This can be easily done by removing -csvout argument to the above command.

If the file contains header line, it is possible to provide mulitple pieces of annotations to genes (rather than just one single column).

To illustrate this, we can check the first two lines (including the header line) of the examplegenefullxref.txt file.

Genename pLi pRec pNull Genefullname Functiondescription Diseasedescription Tissuespecificity(Uniprot) Expression(egenetics) Expression(GNFAtlas) P(HI) P(rec) RVIS RVISpercentile GDI GDI-Phred.

You can run the same command above but change -xreffile from genexref.txt to genefullxref.txt, and the result file can be downloaded from here.

You can open the new VCF file in a text editor and check what has been changed in the file: the INFO field in the VCF file now contains annotations that you need, starting with the string ANNOVARDATE and ending with the notation ALLELEEND.

If multiple alleles are in the same locus, you will see multiple such notations in the INFO field.

We can go to the ANNOVAR directory, then run the following three commands one by one.

Examine the ex1.avinput file to see the simple text format, one variant per line.

Eiu Bio Excel Tutorial For Beginners On A Mac