Currently we define a custom RASSIGN sample field which is the (float value) "Approximate number of reads assigned to each haplotype by MEC score".
This is somewhat similar to the AD sample field in the VCF spec which is defined as the (integer values) "Read depth for each allele".
NOTE: RASSIGN estimates counts for alleles in the called genotype (including replicate alleles) where AD is calculated for all known alleles at that locus.
AD could also be estimated by MEC based assignment and the results either rounded or floored to produce integer results.
This would involve storing sample read distribution arrays until all samples have been assembled and called.
timothymillar
commented
3 years ago
Currently we define a custom
RASSIGNsample field which is the (float value) "Approximate number of reads assigned to each haplotype by MEC score". This is somewhat similar to theADsample field in the VCF spec which is defined as the (integer values) "Read depth for each allele". NOTE:RASSIGNestimates counts for alleles in the called genotype (including replicate alleles) whereADis calculated for all known alleles at that locus.ADcould also be estimated by MEC based assignment and the results either rounded or floored to produce integer results. This would involve storing sample read distribution arrays until all samples have been assembled and called.