Artemis Can'T Read My Vcf File
2
0
Entering edit mode
12.3 years ago
bioinfo ▴ 840

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 • 5.5k views
ADD COMMENT
0
Entering edit mode

any error or message reported?

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
12.3 years ago
bioinfo ▴ 840

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 COMMENT

Login before adding your answer.

Traffic: 2184 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6