excord
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
usage
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.
Ack
excord is developed as part of the company base2 genomics.