Question: Artemis Can'T Read My Vcf File
0
gravatar for bioinfo
6.8 years ago by
bioinfo690
EU
bioinfo690 wrote:

By using BWA and GATK, I have made a vcf file of my raw SNPs. Then I filtered that and kept just homozygous SNPs in my new vcf file with all the header information. Then I compressed and indexed my vcf file and trying to read the vcf.gz file on Artemis but it's not reading my new filtered vcf.gz file though still it can read my raw vcf.gz file.

vcf bam snp • 3.1k views
ADD COMMENTlink modified 5.9 years ago by Biostar ♦♦ 20 • written 6.8 years ago by bioinfo690

any error or message reported?

ADD REPLYlink written 6.8 years ago by JC7.8k

No...when I read the bam or my raw vcf.gz it gives a clear section on the top of the Artemis window with reads/snps in graphics with coverage what we see in IGV but when I read my filtered one it doesn't show that.

ADD REPLYlink written 6.8 years ago by bioinfo690

Does IGV load the new VCF without complaint? Does the VCF validate? http://vcftools.sourceforge.net/docs.html#validator

ADD REPLYlink written 6.8 years ago by Daniel Swan13k

VCF validated the file..I didn't try on IGV...!! but artemis should read it..the file looks ok on the screen though

ADD REPLYlink written 6.8 years ago by bioinfo690
1
gravatar for bioinfo
6.7 years ago by
bioinfo690
EU
bioinfo690 wrote:

The SNP and INDEL files I produced using GATK was error-free but during compressing and indexing steps I did the mistake. The VCF files need to be compressed and indexed using bgzip and tabix as below:

bgzip file.vcf (will create file.vcf.gz)
tabix -p vcf file.vcf.gz (will create file.vcf.gz.tbi)

I didn't use the (-p vcf) flag so it didn't work on artemis as it didn't recognize the vcf file. I had a chat with the author of Artemis Tim Carver who guided me all the way. Thanks Tim.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by bioinfo690
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