https://github.com/brentp/excord

extract SV signal from a BAM
https://github.com/brentp/excord

genomics structural-variation

Last synced: 3 months ago
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extract SV signal from a BAM

• Host: GitHub
• URL: https://github.com/brentp/excord
• Owner: brentp
• License: apache-2.0
• Created: 2017-10-16T15:50:34.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2018-07-26T19:39:50.000Z (over 6 years ago)
• Last Synced: 2024-09-20T00:04:15.986Z (4 months ago)
• Topics: genomics, structural-variation
• Language: Go
• Size: 18.6 KB
• Stars: 11
• Watchers: 4
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-bio-go - excord

README

        
# 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](https://github.com/ryanlayer/stix)

## 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:

```

 | 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.