Experimental tool that aligns sequencing reads to set of haplotypes / templates #8305
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| * FlowPairHMM and FlowBasedAlignment (FBA), but can be easily extended. | ||
| * At present, there are two output formats that can be specified using parameter --output-format: extended and concise. | ||
| * The extended format contains a readxhaplotype matrix that shows alignment score of each read versus each haplotype. | ||
| * Condensed format will following columns (not nessarily in this order) for each processed read: |
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| * Condensed format will following columns (not nessarily in this order) for each processed read: | |
| * Condensed format contains the following columns (not nessarily in this order) for each processed read: |
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Do you mean the columns are in any order? It looks like they're in a fixed order from the writer.
| * | ||
| * <h3>Usage examples</h3> | ||
| * <pre> | ||
| * java -Xms3000m -jar ~{gitc_path}/GATK_ultima.jar FlowPairHMMAlignReadsToHaplotypes \ |
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| * java -Xms3000m -jar ~{gitc_path}/GATK_ultima.jar FlowPairHMMAlignReadsToHaplotypes \ | |
| * gatk FlowPairHMMAlignReadsToHaplotypes \ |
| * <pre> | ||
| * java -Xms3000m -jar ~{gitc_path}/GATK_ultima.jar FlowPairHMMAlignReadsToHaplotypes \ | ||
| * -H ~{haplotype_list} -O ~{base_file_name}.matches.tsv \ | ||
| * -I ~{input_bam} "--flow-use-t0-tag -E FBA \ |
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| * -I ~{input_bam} "--flow-use-t0-tag -E FBA \ | |
| * -I ~{input_bam} --flow-use-t0-tag -E FBA \ |
| * -H ~{haplotype_list} -O ~{base_file_name}.matches.tsv \ | ||
| * -I ~{input_bam} "--flow-use-t0-tag -E FBA \ | ||
| * --flow-fill-empty-bins-value 0.00001 --flow-probability-threshold 0.00001 \ | ||
| * --flow-likelihood-optimized-comp" |
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| * --flow-likelihood-optimized-comp" | |
| * --flow-likelihood-optimized-comp |
| private static final Logger logger = LogManager.getLogger(FlowPairHMMAlignReadsToHaplotypes.class); | ||
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| @Argument(fullName = "haplotypes", shortName = "H", doc="Fasta file with haplotypes") | ||
| public GATKPath haplotypesFa; |
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These can all be public static final
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java does not like that - it says that the variable may not have been initialized
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java does not like that - it says that the variable may not have been initialized
| @Argument(fullName = "output-format", doc="concise or expanded output format: " + | ||
| "expanded - output full read x haplotype, concise - output for each read best haplotype and " + | ||
| "score differences from the next best and the reference haplotype", optional=true) | ||
| public String outputFormat = "expanded"; |
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This should probably be an enum. Or since there's only two options you could make it a boolean with "expanded" as the default (eg. Boolean conciseOutputFormat = false)
Same comment below for the aligner argument.
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Good point, fixed!
| public FlowBasedAlignmentArgumentCollection fbargs = new FlowBasedAlignmentArgumentCollection(); | ||
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| @ArgumentCollection |
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| LikelihoodEngineArgumentCollection likelihoodArgs = new LikelihoodEngineArgumentCollection(); | ||
| SAMFileHeader sequenceHeader; |
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I think you can make these private static final
...adinstitute/hellbender/tools/walkers/haplotypecaller/FlowBasedAlignmentLikelihoodEngine.java
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| //in general reads are already trimmed to the haplotype starts and ends so diff_left <= 0 and diff_right <= 0 | ||
| fbr.applyBaseClipping(Math.max(0, diffLeft), Math.max(diffRight, 0), false); | ||
| } | ||
| // final int haplotypeStart = processedHaplotypes.get(0).getStart(); |
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Should this be uncommented?
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This actually is not necessary in the context of the GATK
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@meganshand - all fixed, PTAL |
This tool is useful for alignment of the reads to a large set of templates that are very close in sequence. In this case the alignment is close to the problem that the HaplotypeCaller is solving - of calculating the likelihood of the read compared to a set of close haplotypes.
The tool outputs read x haplotype matrix for a set of reads and haplotypes using either FlowPairHMM or FlowBasedAlignmentEngine