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Old 03-10-2014, 08:05 AM   #1
Baoqing
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Location: Texas

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Default visualization of vcf in R

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!
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Old 03-10-2014, 08:09 AM   #2
Baoqing
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Default

never mind, i seemed to find the answer here, sorry for the inconveniences
http://www.biostars.org/p/78444/
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