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Artemis Can'T Read My Vcf File

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
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updated by Biostar Biostar • written by bioinfo bioinfo

any error or message reported?

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written by JC JC

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.

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written by bioinfo bioinfo

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

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written by bioinfo bioinfo

2 answers

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.

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written by bioinfo bioinfo

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.

• 0 views • link
written by bioinfo bioinfo

please remove this answer and add as a comment/reply.

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written by Sukhi Singh Sukhi Singh

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