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Documentation on VCI files? Or convert VCI to VCF?

I never came across a VCI file and I'm having some trouble finding documentation on the format. Is anyone familiar with these files?

IsANCHOR the reference allele, why is it absent for some variants? This is from one of the founders for the DO mouse lines. 

##CREATION_TIME=05/23/2016 18:21:16
##INPUT_VCF=/data/cgd/Sanger/REL-1505/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz
##INPUT_VCF=/data/cgd/Sanger/REL-1505/mgp.v5.merged.snps_all.dbSNP142.vcf.gz
##STRAIN=WSB_EiJ
##VCF_KEEP=False
##FILTER_PASSED=False
##FILTER_QUALITY=False
##DIPLOID=False
##PROCESSES=32
#CHROM  POS     ANCHOR  INS     DEL     FRAG
1       3000019 G       .       A       3000019
1       3000023 .       C       A       .
1       3000126 .       G       T       .
1       3000258 G       .       T       239
1       3000287 .       A       G       .
1       3000325 .       G       T       .
1       3000441 .       T       G       .
1       3000470 T       G       .       212
1       3000618 .       G       A       .
1       3000802 .       C       A       .
1       3003197 A       .       G       2726
vci vcf
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written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

Where did you obtain this file? What are the DO mouse lines?

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written by h.mon h.mon

Diversity Outbred cohort of mouse lines that are derived from 8 founder strains. These mice are extremely genetically diverse, like a SNP every 600bp. I found this file from a FTP server for a lab at Jax

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written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

1 answer

I think VCI is a format from the g2gtools package. It is created from vcf files. Apparently, there is no documentation yet, but you may read the vcf2vci code to understand it.

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written by h.mon h.mon

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