Loci with multiple motifs at same position

[christopher-schroeder]

I have called a bunch of samples with straglr and merged the (chrom, start, end, motif) beds into one unified bed. I would like to use this merged bed to genotype each sample again. Sometimes different motifs occur at the same position, but straglr only calles one of them multiple Times. Example:

Here is a position of the merged bed file with multiple motifs at the same position.

$ cat results/str_candidates/merged.bed | grep 56828456
Y	56828456	56836900	CATTC
Y	56828456	56836900	TCCAT

I use this bed for genotyping. What I see:

$ cat results/str/818-13.bed | grep 56828456
Y	56828456	56836900	TCCAT	9286.5	1857.3	55	2907.0	581.4	13
Y	56828456	56836900	TCCAT	9286.5	1857.3	55	2907.0	581.4	13

What I am expecting:

$ cat results/str/818-13.bed | grep 56828456
Y	56828456	56836900	CATTC	...	...	...	...	...	...
Y	56828456	56836900	TCCAT	9286.5	1857.3	55	2907.0	581.4	13