Keep only read pairs with insert length less than or equal to the given value
Category Read Filters
OverviewKeep only read pairs (0x1) with absolute insert length less than or equal to the given value.
Taking absolute values allows inclusion of pairs where the mate of the read being considered is at a smaller genomic coordinate. Insert length is the difference between the 5' outer ends of mates, akin to a SAM record's TLEN (column 9). Length is zero for single-end reads or when the information is unavailable.
FragmentLengthReadFilter specific arguments
|Argument name(s)||Default value||Summary|
|Optional Tool Arguments|
||1000000||Maximum length of fragment (insert size)|
Maximum length of fragment (insert size)
int 1000000 [ [ -∞ ∞ ] ]
GATK version 188.8.131.52 built at 02-13-2019 02:13:49.