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Search: Posts Made By: AllanLindh
Forum: Bioinformatics 04-18-2012, 08:24 PM
Replies: 1
Views: 2,918
Posted By AllanLindh
The problem is with a mismatch between the vcf...

The problem is with a mismatch between the vcf format output by samtools/bcftools view, and the input file expected by vcf-concat. Example:...
Forum: Bioinformatics 04-11-2012, 05:22 PM
Replies: 9
Views: 1,887
Posted By AllanLindh
How to combine .vcf files into whole genome

This discussion is very useful, but when I run mpileup plus bcftools to produce .vcf files for individual Chrm, I have found no way to combine them into whole genome .vcf file for further processing....
Forum: Bioinformatics 04-09-2012, 12:42 AM
Replies: 1
Views: 3,116
Posted By AllanLindh
Parameter order

I suspect you have long since figured this out, but while your command line agrees with the order show in the doc, all the examples have the vcf file before the options. Is it also possible that...
Forum: Bioinformatics 04-07-2012, 11:33 PM
Replies: 1
Views: 2,918
Posted By AllanLindh
Problem with vcf-concat

I am trying to concatenate vcf files from individual Chrm using vcf-concat
no matter what I try, i get following error message and no concatenated file

The column names do not agree in...
Forum: Introductions 04-06-2012, 11:39 PM
Replies: 373
Views: 109,965
Posted By AllanLindh
Concatenating vcf files

Hi y'all. I'm a retired old guy who spent his whole life wishing that genomics would come along, now it's here and I'm almost too old. But I have some data, a linux system, and some software...
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