Details
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Type:
Task
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1.5
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Epic Link:
Description
Situation: We talked to a number of people at ASHG2024 that were interested in visualizing phasing in IGB.
In brief, phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes. PacBio has posted a blog with a lot of useful information about haplotypes and phasing which can be found here: https://www.pacb.com/blog/ploidy-haplotypes-and-phasing/
We know that VCF files contain phasing information, but since those files only contain variant information, they likely wouldn't be useful for visualizing phasing across reads. Instead, we know that PacBio and possibly some other long read sequencing platforms (Illumina?) provide phasing information, but it's unclear if that information is contained in a BAM file or if it's a separate analysis that PacBio has to do.
Task: Look into how IGV displays phasing data: https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/. Use their example dataset to compare how this data is currently being displayed in IGV vs IGB. Examine the files, if possible, to see what the format of this PacBio output is.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-440 [ 15498 ] |
| Description |
*Situation:* We talked to a number of people at ASHG2024 that were interested in visualizing phasing in IGB.
In brief, phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes. PacBio has posted a blog with a lot of useful information about haplotypes and phasing which can be found here: https://www.pacb.com/blog/ploidy-haplotypes-and-phasing/ We know that VCF files contain phasing information, but since those files only contain variant information, they likely wouldn't be useful for visualizing phasing across reads. Instead, we know that PacBio and possibly some other long read sequencing platforms (Illumina?) provide phasing information, but it's unclear if that information is contained in a BAM file or if it's a separate analysis that PacBio has to do. *Task:* Obtain a dataset from PacBio and investigate what those BAM files contain. Investigate other sequencing companies that might provide phasing information, too. Look into how IGV displays phasing data: https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/ |
*Situation:* We talked to a number of people at ASHG2024 that were interested in visualizing phasing in IGB.
In brief, phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes. PacBio has posted a blog with a lot of useful information about haplotypes and phasing which can be found here: https://www.pacb.com/blog/ploidy-haplotypes-and-phasing/ We know that VCF files contain phasing information, but since those files only contain variant information, they likely wouldn't be useful for visualizing phasing across reads. Instead, we know that PacBio and possibly some other long read sequencing platforms (Illumina?) provide phasing information, but it's unclear if that information is contained in a BAM file or if it's a separate analysis that PacBio has to do. *Task:* Look into how IGV displays phasing data: https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/. Use their example dataset to compare how this data is currently being displayed in IGV vs IGB. Exam |
| Description |
*Situation:* We talked to a number of people at ASHG2024 that were interested in visualizing phasing in IGB.
In brief, phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes. PacBio has posted a blog with a lot of useful information about haplotypes and phasing which can be found here: https://www.pacb.com/blog/ploidy-haplotypes-and-phasing/ We know that VCF files contain phasing information, but since those files only contain variant information, they likely wouldn't be useful for visualizing phasing across reads. Instead, we know that PacBio and possibly some other long read sequencing platforms (Illumina?) provide phasing information, but it's unclear if that information is contained in a BAM file or if it's a separate analysis that PacBio has to do. *Task:* Look into how IGV displays phasing data: https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/. Use their example dataset to compare how this data is currently being displayed in IGV vs IGB. Exam |
*Situation:* We talked to a number of people at ASHG2024 that were interested in visualizing phasing in IGB.
In brief, phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes. PacBio has posted a blog with a lot of useful information about haplotypes and phasing which can be found here: https://www.pacb.com/blog/ploidy-haplotypes-and-phasing/ We know that VCF files contain phasing information, but since those files only contain variant information, they likely wouldn't be useful for visualizing phasing across reads. Instead, we know that PacBio and possibly some other long read sequencing platforms (Illumina?) provide phasing information, but it's unclear if that information is contained in a BAM file or if it's a separate analysis that PacBio has to do. *Task:* Look into how IGV displays phasing data: https://www.pacb.com/blog/igv-3-improves-support-pacbio-long-reads/. Use their example dataset to compare how this data is currently being displayed in IGV vs IGB. Examine the files, if possible, to see what the format of this PacBio output is. |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Sprint | Spring 2 [ 211 ] |
| Rank | Ranked lower |
| Sprint | Spring 2 [ 211 ] | Spring 1 [ 210 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 1 [ 210 ] |
10X Genomics has a haplotype browser: https://support.10xgenomics.com/genome-exome/software/visualization/latest/haplotype-browser