Genotyping amplicons?

[adbeggs]

Hi,

Thanks for a great tool. I am playing around with genotyping amplicon data from Nanopore sequencing. I can get Straglr to call certain STRs but not others, and I wonder if I need to do something differently. I have tried changing motifs, positions of the sequence, etc, but I have yet to be successful. Are there any suggestions you can give, please?

I've attached an example file aligned to grch38, and I'm running straglr (latest version) thus:

straglr.py barcode32.new.sorted.bam genome.fa batch1 --genotype_in_size --min_support 1 --loci strtest.bed --max_str_len 1000 --max_num_clusters 2 --nprocs 8

And I get:

#chrom	start	end	repeat_unit	allele1:size	allele1:copy_number	allele1:support	allele2:size	allele2:copy_number	allele2:support
chr1	204156332	204156364	ACAG	31.0	7.8	8	-	-	-
chr11	2171086	2171116	TGAA	32.1	8.0	13	-	-	-
chr5	150076322	150076397	CTAT	68.4	17.1	139	-	-	-
chrX	134481492	134481561	TCTA	72.5	18.1	2	-	-	-
chrX	67545317	67545419	GCA	94.4	31.5	7	-	-	-

str.tar.gz Uploading str.tar.gz…

[readmanchiu]

Thanks for trying Straglr. This is my first time seeing amplicon data, and the main issue is that each read can cover >1 locus. This violates my assumption of each read (the majority of it) covering 1 locus only when checking the alignment CIGAR string. A lot of noise will creep in if this screen on alignments were not made. A separate targeted amplicon mode will need to be implemented to handle this datatype.