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Old 03-15-2012, 09:33 PM   #1
lg36
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Location: london

Join Date: Mar 2012
Posts: 12
Default Viewing vcf and bam files in artemis

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.
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Old 08-21-2012, 06:22 AM   #2
palc
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Location: Auckland, New Zealand

Join Date: Jun 2012
Posts: 6
Default problem with vcf file reading on artemis

I got the same problem..still trying to fix it up
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Old 03-25-2014, 02:24 AM   #3
alyamahmoud
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Location: Egypt, Saudi Arabia

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Posts: 29
Default

you need to zip your VCF file first and then index
bgzip file.vcf
tabix file.vcf.gz
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Old 04-10-2017, 03:44 AM   #4
strepthroat
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Location: Cambridgeshire

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Default

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
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