I am importing vcf files which contains standard chromosome names but also some ambiguous.
Is there a way to preserve all lines which have invalid_loci and are not supported/default for the genome
mt = hl.methods.import_vcf(input_vcf, contig_recoding=recode, force_bgz=True, skip_invalid_loci=True)
For example if the vcf file have chromosome name such as chr1_r3r3r, how can I still save somehow these lines? For example to save the lines with invalid_loci in second matrixtable?