Question: Error VCF- VCFintersect
0
gravatar for ginlucks
2.5 years ago by
ginlucks10
European Union
ginlucks10 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 • 711 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson22k • written 2.5 years ago by ginlucks10
0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson22k 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 COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson22k
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