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Dear Mr. Hartley,
I run the junctionSeq on a cohort with 68 libraries and chose the **use.multigene.aggregates=TRUE** mode. Somehow in the result all bins in gene LY75 (ENSG00000223972+ENSG00000227…
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WH version= 1.4
Hello! I have HiFi reads from PB and diploid assembly
I make two vcf files with DeepVariant (dv.vcf) and find_snv_candidates (hifi_on_primary_find_snp.vcf ). Then I genotyped b…
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Hello,
I am running PsiCLASS on 43 RNA-Seq samples from Arabidopsis Thaliana. The whole run completes very fast and also produces quite good results. I compared the assemblies from PsiCLASS with th…
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Hello,
Is it possible to get multiple BAM files to appear while using the --track-config option?
My code chunk looks like this:
```
create_report \
--fasta $genome_fasta \
--output "${…
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In my hands, display of .bed files disallows setting the track height below 40 either interactively or using, e.g., maxHeightPixels=15:15:15 in the trackline.
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`chr3 101703348 Minda_95 N . PASS SVLEN=3190;SVTYPE=DEL;SUPP_VEC=PB_ID_51866_2,PB_d_315,ONT_ID_11133_2,ONT_d_150,ILL_MantaDEL:64089:0:1:0:0:0,PB_severus_DEL4753,ONT_severus_DEL5502,PB_Sniffles2.DEL.2…
jzook updated
2 months ago
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The VCF parser is currently unable to parse VCFs with complex rearragnements and this is showing up as Picard issues: https://github.com/broadinstitute/picard/issues/1406
Need to prioritize and fix…
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ONT duplex reads have RNAMEs in the form of ;. Sniffles naively outputs this into VCF when you use the `--output-rnames` flag without escaping the ; meaning that VCF parsers think the second read name…
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I ran a slightly modified test example:
```
source configuration.env
KETREW_CONFIGURATION=_kclient_config/configuration.ml; DREAM=https://storage.googleapis.com/dream-challenge; ocaml run_pipeline.…