Add a description of the toolkit to the README #34
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nh13
requested changes
Mar 14, 2024
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@nh13 ready for a re-review when you have time! Thanks! |
msto
requested changes
May 10, 2024
README.md
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| The tool [`fgsv SvPileup`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/SvPileup.md) takes a query-grouped BAM file as input and scans through each template one at a time, where a template is the full collection of reads and alignments from a single source molecule. | ||
| For example, a paired-end read may have an alignment per read: one alignment for read 1 and another alignment for read 2. | ||
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| Primary and supplementary alignments for a template (see the [SAM Format Specification v1](https://samtools.github.io/hts-specs/SAMv1.pdf) for more information) are used to construct a “chain” of aligned sub-segments in a way that honors the logical ordering of sub-segments and their strandeness in relation to the reference sequence. |
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introduce template here, or swap to queryname/group?
| --output sample.svpileup.aggregate.txt | ||
| ``` | ||
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| Because of variability in typical short-read alignments, evidence for a single breakpoint may span a few loci near the true breakend loci. For example, if the breakpoint only has intra-read evidence, then the breakpoint could coincidentally occur within the unobserved bases between read 1 and read 2 in a pair. In other cases and due to sequence similarity or homology between each breakend locus, it is not always possible to locate the exact nucleotide point where the breakends occur, and instead a plausible region may exist that supports either breakend loci. |
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| Because of variability in typical short-read alignments, evidence for a single breakpoint may span a few loci near the true breakend loci. For example, if the breakpoint only has intra-read evidence, then the breakpoint could coincidentally occur within the unobserved bases between read 1 and read 2 in a pair. In other cases and due to sequence similarity or homology between each breakend locus, it is not always possible to locate the exact nucleotide point where the breakends occur, and instead a plausible region may exist that supports either breakend loci. | |
| Because of variability in typical short-read alignments, evidence for a single breakpoint may span a few loci near the true breakend loci. For example, if the breakpoint only has paired-end evidence, then the breakpoint could coincidentally occur within the unobserved bases between read 1 and read 2 in a pair. In other cases and due to sequence similarity or homology between each breakend locus, it is not always possible to locate the exact nucleotide point where the breakends occur, and instead a plausible region may exist that supports either breakend loci. |
or inter-read, but I find split-read and paired-end to be more familiar terms
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I've read this a few times and don't quite understand what it's saying
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| Because of variability in typical short-read alignments, evidence for a single breakpoint may span a few loci near the true breakend loci. For example, if the breakpoint only has intra-read evidence, then the breakpoint could coincidentally occur within the unobserved bases between read 1 and read 2 in a pair. In other cases and due to sequence similarity or homology between each breakend locus, it is not always possible to locate the exact nucleotide point where the breakends occur, and instead a plausible region may exist that supports either breakend loci. | ||
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| The tool [`fgsv AggregateSvPileup`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/AggregateSvPileup.md) is used to coalesce nearby breakpoints into one event if they appear to belong to one true breakpoint. |
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| The tool [`fgsv AggregateSvPileup`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/AggregateSvPileup.md) is used to coalesce nearby breakpoints into one event if they appear to belong to one true breakpoint. | |
| The tool [`fgsv AggregateSvPileup`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/AggregateSvPileup.md) is used to coalesce pileups in proximity to each other into one event if they appear to support the same breakpoint. |
| The tool [`fgsv AggregateSvPileup`](https://github.com/fulcrumgenomics/fgsv/blob/main/docs/tools/AggregateSvPileup.md) is used to coalesce nearby breakpoints into one event if they appear to belong to one true breakpoint. | ||
| This polishing step preserves true positive breakpoint events and intends to reduce the number of false positive breakpoint events. | ||
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| Adjacent breakpoints are only merged if their left breakends map to the same reference sequence, their right breakends map to the same reference sequence, the strandedness of the left and right aligned sub-segments is the same, and their left and right genomic breakend positions are both within a given length threshold. |
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| Adjacent breakpoints are only merged if their left breakends map to the same reference sequence, their right breakends map to the same reference sequence, the strandedness of the left and right aligned sub-segments is the same, and their left and right genomic breakend positions are both within a given length threshold. | |
| Adjacent breakpoints are only merged if their left breakends map to the same strand of the same reference chromosome (or contig), their right breakends map to the same strand of the same reference chromosome (or contig), and their left and right genomic breakend positions are both within a given length threshold. |
Also, what is the threshold?
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| One shortcoming of the existing behavior, which should be corrected at some point, is that intra-read breakpoint evidence is considered similarly to inter-pair breakpoint evidence even though intra-read breakpoint evidence often has nucleotide-level alignment resolution and inter-pair breakpoint evidence does not. | ||
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| The output of this tool is a metrics file tabulating the coalesced breakpoints with all previous breakpoint IDs listed for the new breakpoint event and an estimation of the allele frequency of the event based on the alignments that support the breakpoint. |
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| The output of this tool is a metrics file tabulating the coalesced breakpoints with all previous breakpoint IDs listed for the new breakpoint event and an estimation of the allele frequency of the event based on the alignments that support the breakpoint. | |
| The output of this tool is a table of coalesced breakpoints. Each aggregate breakpoint is annotated with the constituent pileup IDs and an estimation of the allele frequency of the breakpoint based on the alignments that support the breakpoint. |
How is allele frequency calculated? Especially without the original bam?
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Enhancing the README to better communicate how this toolkit works and should be used.