clintval / vartovcf / 37144445843

98%

push

github

feat: write VarDict's repeat context as INFO REPEAT_UNIT_COPIES and REPEAT_UNIT_LEN (#118)

REPEAT_UNIT_COPIES and REPEAT_UNIT_LEN are VarDict's MSI and MSILEN columns: the copies of the 1-6 bp tandem repeat unit next to the variant, and that unit's length. They describe sequence context, not microsatellite instability, so they get names that say so. Both are INFO, Number=A, and absent when VarDict did not compute them (it writes 0) or there is no ALT allele. The Description states VarDict's one-sided anchoring, and that the count can be fractional when VarDict raises it to an indel's 3' shift over its length.

18 of 18 new or added lines in 2 files covered. (100.0%)

644 of 661 relevant lines covered (97.43%)

31.72 hits per line