Loci skipped with SourceSeq mapping.

[rajwanir]

A separate issue from the results in #64 is that 0.5-0.8% of markers could not be mapped from hg19 to hg38. While I think some percentage will be skipped anyway. Do you have any suggestions to reduce this number of skipped loci?

Currently I think, one of the issue might be that mappings are made to the no ALT version (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.) which is necessary but could filter the snps on ALT contigs. A possible workaround could be to try a two step alignment, first align to choromosomal assembly (no_alt) and then sequences that don't align can be mapped to primary assembly. Is the something you think might be feasible with the current version of gtc2vcf with just by piping or parameter change?

The second option might be to use an alt-aware aligner (https://github.com/lh3/bwa/blob/master/README-alt.md).

Wanted to check if you have any thoughts or suggestions on this. Thanks.