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straglr_compare.md

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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)