VariantToolChest
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mebbert
VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerful t...
Hello, Thanks for developing the tool! I used the association test argument and everything went through smoothly. But the results file contains only a part of the original variant sites....
Hi Mark, I used Variant Tool Chest to make an intersection between two samples in a VCF file. I have rsIDs for my variations but the resultant data misses them....
Not so much an issue, but rather a question. Came across your BMC Bioinf paper, I am attempting to compare genotype concordance between samples (monozygotic twins) in a vcf (similar...
Hi, Have run into a NumberFormatException running Ion Torrent VCF files. Neither the supplied test VCF (TSVC_variants.vcf.gz) nor any of my own work, and I get the same error: ```...
``` javascript $ java -jar VariantToolChest-0.9-SNAPSHOT-jar-with-dependencies.jar VarStats -i /home/blab/Desktop/matK/samtool_result/matK.raw.vcf -s T 2015-07-02 18:50:25 INFO VarStatsEngine:91 - Namespace(SUMMARY=T, association=false, VCF=[/home/blab/Desktop/matK/samtool_result/matK.raw.vcf], OUTPUT=null, pheno=null, DETAILED=null) 2015-07-02 18:50:25 INFO AbstractVariantPool:134 - Opening /home/blab/Desktop/matK/samtool_result/matK.raw.vcf for...
Hello, I've been running into exceptions while trying out some set operations with empty datasets. The program does work perfectly on any other operations. Reference genome directory contains .fa as...
