Bug in creation outputvcf file after Beagle
Posted in Ask the team | Last updated on 2012-10-23 18:27:35


Comments (8)

Hi,

I used Beagle to phase my data but for some indels, I have some probleme :

example :

Input vcf :

2       68599872        .       ATG     A       14.40   PASS    AC=1;AC1=1;AF=0.028

Input for beagle created by ProduceBeagleInput:

2:68599872 TG - 1.0000 0.0000 0.0000 ......

Output vcf created by BeagleOutputToVCF:

2       68599872        .       ATG     .       14.40   BGL_RM_WAS_-    AC1=1;AF1=0.02965.....

error message by CombineVariants:

MESSAGE: Badly formed variant context at location 68599872 in contig 2. Reference length must be at most one base shorter than location size

Can you help me?

Tipahine


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