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Question: Error VCF- VCFintersect
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gravatar for ginlucks
3.7 years ago by
ginlucks • 10
European Union
ginlucks • 10 wrote:

Hello,

I'm try to select shared variant between patients using VCF-VCFintersect but appear this error message:

unable to find FASTA index entry for 'M'

if I use hg_g1k as reference genome

or

unable to find FASTA index entry for '1'

If I sue hg19 as reference genome

thanks in advance for any help

 
fasta M vcf intersect • 1.0k views
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modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by ginlucks • 10
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The issue is a genome mismatch problem. "hg_g1k_b37" is from 1000 Genomes and with a mitochondrial chromosome named as "MT".  "hg19" is from UCSC and uses chromosome named like "chr1, chr2, ...chrM, chrX...".  More about this type of mismatch is here:
http://wiki.galaxyproject.org/Support#Reference_genomes

Use the same exact reference genome with tools as the VCF datasets were created against. Perhaps the version from Ensembl? If needed, load it as a custom reference genome and use it that way. Instructions:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Best, Jen, Galaxy team

 

 

 
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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