vcf verbose output #27
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If `--output_all_positions` is passed to `merge_to_vcf`, the output VCF will include all positions covered by the reference: sites with intrahost variants and sites with consensus calls but no sub-consensus variation. Per-sample consensus calls (relative to the reference) will be included. Positions not represented in the assembly for each sample will be omitted. This flag is not included by default. A unit test is added to test_intrahost.py::test_output_all_positions.
….0, not . (missing)
call iSNVs via vPhaser2 within assemble_refbased.wdl. iSNV calling should be scheduled to occur in parallel with align-to-self depends on merge of this PR upstream and release of docker image: broadinstitute/viral-phylo#27
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Oof... this is wading into the thick of some tricky code.. I think I might benefit from a live discussion on it as I try to remember all the bits going on here. One quick clarification: this code path is only (currently) used for intrahost variant calling via vphaser, right? Not used for assembly consensus calling, and in theory, is unnecesary for isnv calling by other variant callers that speak vcf more natively? |
| self.assertEqual(rows[3].ref, 'G') | ||
| self.assertEqual(rows[3].alt, 'C') | ||
| self.assertEqual(':'.join(rows[3][0].split(':')[:2]), '1:1.0') | ||
| self.assertEqual(':'.join(rows[3][1].split(':')[:2]), '0:0.0') |
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This should maybe be self.assertEqual(':'.join(rows[3][1].split(':')[:2]), '0:.') for positions we are imputing from ref, since absence of iSNVs in the vphaser output does not necessarily mean iSNVs were absent, only that they did not warrant inclusion in the output.
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Sure thing; happy to connect about this. To answer your question: yeah, this code path is only for vphaser currently. It's not used for assembly consensus calling, through the changes here are perhaps a step in that direction (outputting all positions in the VCF if this new toggle is set). We may still want to parse/interpret the output of other variant callers ourselves, either for consensus calling or for merging sample data (as an example, |
If
--output_all_positionsis passed tomerge_to_vcf, the output VCF will include all positions covered by the reference: sites with intrahost variants and sites with consensus calls but no sub-consensus variation. Per-sample consensus calls (relative to the reference) will be included. Positions not represented in the assembly for each sample will be omitted. This flag is not included by default. A unit test is added to test_intrahost.py::test_output_all_positions.