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Median fragment length of reads supporting each allele (MFRL)

Category Variant Annotations


Median fragment length of reads supporting each allele.

The output is an array containing, for each allele, the median fragment length (this is synonymous with "insert size") over all reads that best match that allele. Fragment length here is defined to be non-negative and is zero for unpaired reads. Thus is annotation is only useful with paired-end sequencing data.

For example, if the left read in a pair starts at position 100 and the right ends at position 300 (inclusive) then the fragment length is 201 regardless of which is read 1 and which is read 2, i.e. it is not -201.

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GATK version built at Wed, 3 Apr 2019 09:19:24 -0400.