SNP annotation

[kamilo889]

Hi all I'M currently performing my first exome sequencing analysis following the GATK pipeline, at this moment I have ended the VQSR and have a final VCF file ... however the question is what is next. (all this performedusing as reference the hg19 genome)

in the web appear 3 options
BEAGLE
SNPeff
Annovar

I use SNPeff using this code:
java -jar snpEff.jar eff -c snpEff.config -v hg19 -o gatk SNP_INDELS_Recalibrated.vcf > SNPeff_final.vcf

when start the run the program selects several variants but also appear this message "Skipping malformed SnpEff effect field....."

I dont know if is due to loss of compatibility or other thing.

After that I've runned the GATK VariantAnnotator and appear a new VCF file ... is this method correct?. Its only one single sample so cant do an analysis with pedigree.

What tool do you recommend? how interprete this data. and how obtain a reliable output maybe an Excel file or other class.

Thanks for your help

[adamyao]

You can try to upload your vcf file to VarioWatch (http://genepipe.ncgm.sinica.edu.tw/v...n.do?mega=true) to see if the annotation can be done.

[kamilo889]

yeah, today I've uploaded my VCF raw to http://gvsbatch.gs.washington.edu/Se...n138/index.jsp and wAnnoVar but I didnt know this tool, also for exome analysis is better to work with B37 or hg19?

after have the data result ... how I can work with it? can I transform it to a Excel file?

Thnak for your reply

[Brian Bushnell]

for exome analysis is better to work with B37 or hg19?

Those are different names for the same thing. There are multiple revisions of it (e.g. 37, 37.1, 37.2, etc) but the coordinates should be compatible. HG20/GRCh38 has now been released for over 6 months, so you should consider that, too. You should use the latest version that is compatible with the rest of your data and pipeline - for example, if you are trying to correlate SNPs with the results of a study based on HG19, then obviously you should use HG19. But if you are starting from scratch, use the latest.