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