I have some exome sequencing data which used an exome capture kit (http://emea.support.illumina.com/downloads/nextera-rapid-capture-exome-v1-2-product-files.html) from Illumina which is based on hg19 coordinates.
I aligned this data to hg38 and called variants etc which worked out fine. However, I now want to look at copy number, which requires explicitly providing the exome regions that were targeted. Since this information is based on hg19 coordinates and my alignments (.bam) are based on hg38, I'm assuming I can't simply ignore the difference and hope to get meaningful results.
My question is, is it perfectly OK to simply lift over the targeted regions .BED file to hg38 (though the liftover tool reports that some regions are lost) or, is it a general rule that if my exome capture is based on hg19 coordinates I should be sticking to the hg19 assembly for analysis?