Sample data

ASSEMBLY_ID    XXXX
#CNV_WINDOW_WIDTH       2000
#COSMIC COSMIC v48
#DBSNP_BUILD    dbSNP build 132
#DGV_VERSION    9
#FORMAT_VERSION 1.7
#GENERATED_AT   XXX
#GENERATED_BY   cgatools
#GENE_ANNOTATIONS       NCBI build 37.2
#GENOME_REFERENCE       NCBI build 37
#MIRBASE_VERSION        miRBase version 16
#PFAM_DATE      XXX
#REPMASK_GENERATED_AT   XXX
#SAMPLE XXX
#SEGDUP_GENERATED_AT    XXX
#SOFTWARE_VERSION       1.12.0.47
#TYPE   VAR-OLPL

>locus  ploidy  chromosome      begin   end     zygosity        varType reference       allele1Seq      allele2Seq      allele1Score    allele2Score    allele1HapLink  allele2HapLink  xRef    evidenceIntervalId      allele1ReadCount        allele2ReadCount        referenceAlleleReadCount        totalReadCount  allele1Gene     allele2Gene     pfam    miRBaseId       repeatMasker    segDupOverlap   relativeCoverage        calledPloidy
1       2       chr1    0       10000   no-call no-ref  =       ?       ?                                                                                                                          
2       2       chr1    10000   11090   no-call complex =       ?       ?                                                                                                                                       1.13    N
3       2       chr1    11090   11105   hom     ref     =       =       =                                                                                                                                       1.13    N
4       2       chr1    11105   11170   no-call complex =       ?       ?                                                                                                                                       1.13    N
5       2       chr1    11170   11195   hom     ref     =       =       =                                                                                                                                       1.13    N
6       2       chr1    11195   11211   no-call complex =       ?       ?                                                                                                                                       1.13    N
7       2       chr1    11211   11227   hom     ref     =       =       =                                                                                                                                       1.13    N

Example

vtools import --format CGA /path/to/masterVarBeta$ID.tsv.bz2 --build hg19