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## Expected Behavior
Tell us what should happen
`cwltool --make-template` should create a valid yaml
## Actual Behavior
Tell us what happens instead
An invalid yaml is created when input t…
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This was posted by an external user:
I am harmonizing WGS data for the GREGoR consortium using the WGS single sample workflow (in dragen_mode) on AnVIL. I've hit a parsing error when reprocessing …
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`chr15 98348348 Minda_47 N . PASS SVLEN=460879;SVTYPE=DUP;SUPP_VEC=ILL_MantaDUP:TANDEM:223247:0:1:0:0:0,ILL_gridss240bf_60h,ONT_severus_DUP2603,PB_ID_20435_2,PB_r_130,ONT_ID_72365_2,ONT_r_96,PB_Sniff…
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Following on from https://github.com/umccr-illumina/dragen/issues/53
vc-enable-phasing is currently running by default in the somatic pipeline and generating FORMAT/PS tags
To enable combing SNVs …
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`chr15 79431718 Minda_45 N . PASS SVLEN=1009;SVTYPE=DEL;SUPP_VEC=ONT_ID_71992_2,ONT_severus_DEL2557,ONT_Sniffles2.DEL.1E2ME,PB_ID_20108_2,PB_severus_DEL2292,PB_d_126,ONT_d_53
`
https://v2.genomeribb…
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`chr4 149325373 Minda_107 N . PASS SVLEN=149743;SVTYPE=DUP;SUPP_VEC=ILL_2463309523:2,ILL_MantaDUP:TANDEM:88580:0:1:0:0:0,ILL_gridss83bf_10453h,PB_severus_BND5384_2,ONT_severus_DUP6210,PB_ID_9242_2,PB…
jzook updated
2 weeks ago
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- [x] try calling with Varscan
-> only calls the insertion but not the deletion....
- [x] dragen + evidence BAM
-> not conclusive, only part of the region covered in evidence BAM. Seems to su…
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Under `dragen_tso_ctdna_step.py` snippet below; we currently remove samples that have qc selected and only include samples that must be tumor.
https://github.com/umccr/data-portal-apis/blob/f790a68…
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Hi @freeseek
I note that there are some indel records that gtc2vcf initially writes them but then `bcftools norm --check-ref x` filters them out. However, I was comparing to the [Dragen array outp…
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The Dragen Hash Table generation Workflow has some differences from other pipelines that require changes to the main Dragen quickstart script so it is not yet supported. It can be added if there is su…