straglr_compare.md

Comparing Straglr results

straglr_compare.py is provided to compare Straglr results from test sample against parent(s) or normal control(s) for detection of de novo expansions:

• corresponding alleles between test and control are found by intersecting their Straglr .tsv outputs using BEDTools. Loci that overlap at least 90% with each other are considered the sa me
• actual sizes or copy numbers (actual_repeat column in .tsv) detected in each supporting read for each test allele are compared against their counterparts in the control using a 2-sam ple t-test
• test alleles deemed to be larger than their counterparts in all control(s) by t-test are reported
• expanded alleles only reported in the test sample but not the control(s) are also reported in the output
• annotation file (GTF) and promoter/enhancer coordinates (BED) can be provided by user so that only expansions overlapping the provided features are reported

Usage

straglr_compare.py <test_straglr.tsv> <control_straglr.tsv> [control_straglr.tsv ...] 

optional parameter	description	Default
use_copy_number	use copy number instead of size	False (i.e. size used)
min_expansion	minimum expansion	100
min_support	minimum number of support reads in sample event	4
skip_chroms	skip results from chromosomes specified (e.g. chrY)	None
pval_cutoff	p-value cutoff for testing T-test hypothesis	0.001
gtf	GTF file of annotation	None
promoters	BED file of promoters	None
enhancers	BED file of enhancers	None
old_version	results from original version (v1.0) of Straglr used (tsv output different)	False

Output

column	description
chrom	chromosome of test allele
start	start coordinate of test allele
end	end coordinate of test allele
repeat	repeat motif of test allele
ref_size	reference size (start - end + 1)
test_allele	allele size (or copy number) in test sample
test_allele_support	number of support reads for test allele in sample
expansion	test_allele - ref_size + 1
control_alleles	control allele size(s)/copy numbers(s) e.g. c1a,c1b;c2a,c2b where c1a and c2a are alleles from control1; c2a,c2b are alleles from control2, etc. "-" if test allele no
t found in control(s)
pvals	t-test p-val of test allele against every control allele. Output format the same as control_alleles. "-" if test allele not found in control(s)