Multiallelic STRs

[themkdemiiir]

Hey, thanks for the great tool. How are you dealing with problems related to multiallelic short tandem repeats? For example, RFC1.

https://github.com/broadinstitute/str-analysis/issues/12#issue-2136249713

[hdashnow]

We make a separate call for each motif. The cis/trans arrangement is uncertain, however.

Here is an example from 1000 genomes, sample HG00103:

#chrom  left    right   repeatunit  allele1_est allele2_est anchored_reads  spanning_reads  spanning_pairs  expected_spanning_pairs spanning_pairs_pctl left_clips  right_clips unplaced_pairs  depth   sum_str_counts
chr4 39348432        39348476        AAGGG   0.00    7.16    0       6       5       39.64   0.01    4       0       0       32.0    35
chr4 39348424        39348483        AAAAG   0.00    36.61   19      0       0       37.33   0.00    1       0       0       32.0    547