I have used CrossMap to lift over vcf files from GRCh37 coordinates to GRCh38. Here is the command:
python CrossMap-0.2.8/bin/CrossMap.py vcf GRCh37_to_GRCh38.chain.gz sample1520.vcf.gz Homo_sapiens.GRCh38.dna.primary_assembly.fa sample1520.N.grch38.vcf
I noticed that for some of my indel calls, for which I have an END coordinate field in the vcf INFO, those coordinates are not lifted over, which is causing me issues in some downstream analyses (see example variant below).
2 240692368 . AG A . PASS AC=1;AF=0.5;AN=2;DEL=.;END=241631786;HOMLEN=0;SVLEN=-1;set=indel GT:AD 0/1:20,6
Is there a way to lift over that field as well? Is there any lift-over tool available which takes care of this issue? I tried UCSC liftover tool, but the same issue occurs.
Any help is appreciated. Thanks!