Viewing vcf and bam files in artemis

[lg36]

Dear All, I'm new to Artemis and could do with some help viewing vcf files.

1) First I loaded my embl reference file
2) Then I index my vcf files with tabix as per the manual
3) Then I go to File > Read BAM/VCF
4) Find the file and select it (but nothing seems to happen in the viewer)

When I click on Display > VCF also nothing happens

I've even tried using bcftools to index the bcf files and upload them but that doesn't work either.

What am I doing wrong? I should be able to load various vcf files?

I'd be really grateful for some guidance on this. Many thanks.

[palc]

problem with vcf file reading on artemis

I got the same problem..still trying to fix it up

[alyamahmoud]

you need to zip your VCF file first and then index
bgzip file.vcf
tabix file.vcf.gz

[strepthroat]

Hi there, I am having a similar problem with my BAM files.

I have some transcriptome data in BAM format (alongside the BAM sorted and sorted.bai index files made with SAM tools).

When i read the BAM file nothing happens on my screen.

Thanks