clintval / vartovcf / 37176777962

98%

push

github

feat: add the HOMOPOLYMER_INDEL and TANDEM_REPEAT_INDEL filters (#123)

Both label an insertion or deletion that adds or removes exactly one repeat unit in a long repeat, the signature of polymerase slippage. HOMOPOLYMER_INDEL covers one-base units and TANDEM_REPEAT_INDEL covers 2-6 bp units; each takes a minimum copy count (--filter-homopolymer-indel, --filter-tandem-repeat-indel) and an optional AF limit (--filter-homopolymer-indel-max-af, --filter-tandem-repeat-indel-max-af), with no AF limit when that is not given. var2vcf_valid.pl applies both branches under one label, MSI12, whose description omits the AF limits and the one-unit condition.

92 of 92 new or added lines in 2 files covered. (100.0%)

866 of 883 relevant lines covered (98.07%)

29.8 hits per line