Visualize Vcf In Igv

Question

[mad.cichlids]

when i was trying to use R to visualize my VCF file I first loaded the file and compressed it:

 vcf <- readVcf(str.vcf, "Genome")
 compressVcf <- bgzip(vcf, tempfile())

but when i run indexTabix

idx <- indexTabix(compressVcf, "vcf")

Error in value[3L] : internal: samtools invoked 'exit(1)'; see warnings() and restart R file: /tmp/RtmpTzJzHz/filea305fdaaade In addition: Warning message: In doTryCatch(return(expr), name, parentenv, handler) : [ti_index_core] the file out of order at line 19

It seems my file is not in order, but what kind of order or how should i sort my vcf or genome ?

Thanks!

[Sean Davis]

Do the chromosome names match EXACTLY between the vcf and the genome?

[mad.cichlids]

It seems my file is not in order, but what kind of order or how should i sort my vcf or genome ?

Answer 1

[mad.cichlids]

never mind, the answer seems lie in this post Tabix -p vcf ERROR