excord extracts split and paired-end reads that are possible indicators of structural variation. It also outputs reference depth.

The output of excord is used as input to stix SV index

By default excord expects stuff from a single chromosome:

excord --fasta $fasta --prefix some/cool/project $bam $chrom | bgzip -c > $out

This will write some/cool/project.rp.bin with reference and pair coverage interleaved.

It's possible to read a bam from stdin and write only the discorants and splitters:

<bam stream> | excord --discordantdistance 500 --fasta $fasta /dev/stdin | bgzip -c > $out

It's not possible to write reference coverage with this mode.

excord is developed as part of the company base2 genomics.