support filtering a VariantCollection according to an intervals list file
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- Dominant language
- Python
- Stars
- 87
- Forks
- 28
- Avg merge
- 3h 27m
- Merged PRs (30d)
- 27
Description
For some of our analyses it would be helpful to be able to filter a VariantCollection to only those variants that fall within the intended capture targets.
Example intervals list:
[odonnt02@minerva4 ~]$ head /sc/orga/projects/ngs/resources/captures/2.3/Human_All_Exon_V5.hg19.interval_list
@HD VN:1.4 SO:unsorted
@SQ SN:chrM LN:16571 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb
@SQ SN:chr1 LN:249250621 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:chr2 LN:243199373 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:a0d9851da00400dec1098a9255ac712e
@SQ SN:chr3 LN:198022430 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:641e4338fa8d52a5b781bd2a2c08d3c3
@SQ SN:chr4 LN:191154276 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:23dccd106897542ad87d2765d28a19a1
@SQ SN:chr5 LN:180915260 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:0740173db9ffd264d728f32784845cd7
@SQ SN:chr6 LN:171115067 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:1d3a93a248d92a729ee764823acbbc6b
@SQ SN:chr7 LN:159138663 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:618366e953d6aaad97dbe4777c29375e
@SQ SN:chr8 LN:146364022 UR:file:/gs01/projects/ngs/resources/gatk/2.3/ucsc.hg19.parmasked.fasta M5:96f514a9929e410c6651697bded59aec
GATK also supports a few other formats (probably not needed here though): https://www.broadinstitute.org/gatk/guide/article?id=1319
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by tracing the VariantCollection filtering entry point and reviewing the issue's interval_list example. Define how the list file is parsed and how variants are retained when they fall within capture targets; done means a VariantCollection can be filtered using this format and the behavior is covered by tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100