#3 Mapping VCF over an inversion doesn't revcomp the alleles

[Dan Bolser]

When lifting over VCF lines the alleles should be revcomp'ed when the alignment is an inversion.

[Liguo Wang]

Hi,
First please make sure you use the most recent version. If the problem persists, please provide a few lines of you VCF file to help trouble shooting. Thanks

[Matthieu]

I have a similar issue in v0.3.3, where the ref allele is indeed the reverse complement but not the alt allele.

command:
CrossMap.py vcf chain/hg19ToHg38.over.chain.gz test.3.vcf genomes/Hsapiens/hg38/seq/hg38.fa test.3.hg38.vcf

Input:

##fileformat=VCFv4.2
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ALS
15      23102357        .      C       A       .       .       .   GT      0/1

Output:

##fileformat=VCFv4.2
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ALS
15      22770732        .      G       A       .       .       .   GT      0/1

Expected output:

##fileformat=VCFv4.2
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ALS
15      22770732        .      G       T       .       .       .   GT      0/1