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Data released on September 13, 2017

Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing"

Pedersen, B, S; Collins, R, L; Talkowski, M, E; Quinlan, A, R (2017): Supporting software for "Indexcov: fast coverage quality control for whole-genome sequencing" GigaScience Database. http://dx.doi.org/10.5524/100349 RIS BibTeX Text

The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at: https://github.com/brentp/goleft under the MIT license.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix090

Additional information:

https://github.com/brentp/goleft

http://indexcov.s3-website-us-east-1.amazonaws.com/

Keywords:

Whole genome sequencing (WGS) copy number variation (CNV) structural variation (SV) sequence coverage 

Software

http://gigadb.org/images/data/cropped/100349.jpg

Funding:

  • Funding body - National Institutes of Health
  • Award ID - R01HG006693
  • Funding body - National Institutes of Health
  • Award ID - U24CA209999

Files: (FTP site) Table Settings

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File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Githubarchive4.79 MB2017-08-25
HTMLzip2.11 MB2017-08-25
HTMLUNKNOWN4 KB2017-08-25
ReadmeTEXT1.46 KB2017-08-25
Displaying 1-4 of 4 File(s).

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