clintval / vartovcf / 37208458247

98%

push

github

feat: add the SAME_READ_POSITION filter (#125)

SAME_READ_POSITION, from --filter-same-read-position, labels a call whose 2 or more ALT reads all place the variant at the same distance from their read ends (ALT_READ_POS_VARIES 0) at an AF below the threshold: the sign of one fragment counted repeatedly or an error at a fixed sequencing cycle. var2vcf_valid.pl applies this as pSTD, with its AF below 0.35 condition unstated, and also labels every single-read call, whose positions cannot vary; this label needs at least 2 ALT reads.

23 of 23 new or added lines in 2 files covered. (100.0%)

913 of 930 relevant lines covered (98.17%)

29.95 hits per line