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`chr5 36023180 Minda_112 N . PASS SVLEN=3336845;SVTYPE=DUP;SUPP_VEC=PB_severus_BND5690_2,PB_r_284,ONT_severus_DUP6554,ONT_r_183,ILL_MantaDUP:TANDEM:97365:0:1:0:0:0,ILL_2945609644:2,ILL_gridss91bf_991…
jzook updated
1 month ago
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**Tasks**
Tasks extracted from PR #94 :
Based on commit 0a30513f360b82828efeed6835f362df999f776a
- [ ] Unify output filenames for Control Freec and CopyWriter.
- [ ] Consolidate GRCh37 and GR…
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Hello,
I have run Sniffles2 in `non-germilne` mode, but it is missing a deletion I was expecting, because it is given by other SV callers (cuteSV, SAVANA, nanomonSV) and because it is present from vi…
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Hello!
I am using strelka2 for calling indels. The indels called by other software and strelka1 all look normal. However, when I look into the output of strelka2, all variants have either very high…
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## Expected Behavior
The workflow should execute successfully creating RO.
## Actual Behavior
Workflow fails with the following error:
`Anonymous file object must have 'contents' and 'basename…
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When running very large sample BAMs through call-sSNV, it likely that the pipeline would fail because of default resource configurations.
Although the `base_resouce_update` function in `template.co…
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Because Crossmap supports INFO/END values in SV VCFs since `0.4.3`, it gives the impression that it supports lifting over of structural variants as well. However it currently doesn't convert values in…
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The joint caller should optionally output a csv file that gives for pairs A, B of variants (both germline and somatic) at each sample:
- total number of fragments (i.e. reads or mates of reads) overla…
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I concatenated the germline and LOH variants called by VarScan and used that in cnvkit call. A 43Mb region was called as a deletion with BAF=0. However, by looking at the SNPs that are 0/1 in normal s…
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## INFO=
# CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
1 726934 . G A 2.21496e-14 PASS SSC=21.1148;AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=133;DPB=133;DPRA=0;EPP=4.0…