Hi,
The realigned bamlet outputed by EH contains a CIGAR string for each read showing the match to the best modified reference. I am wondering if it would be possible to get a CIGAR string outputed for the second best reference match as well? We could then use the difference between the best and second best match as a quality control measure to identify more questionable genotype calls. This would be useful when working with large catalogs, where some loci will have flanking regions similar to the repeat.
Thanks
Hi, The realigned bamlet outputed by EH contains a CIGAR string for each read showing the match to the best modified reference. I am wondering if it would be possible to get a CIGAR string outputed for the second best reference match as well? We could then use the difference between the best and second best match as a quality control measure to identify more questionable genotype calls. This would be useful when working with large catalogs, where some loci will have flanking regions similar to the repeat. Thanks