James Hashfield

Can I use MosaicForecast for ~30X WGS dataset?

1

Hi, I used DeepMosaic to detect mosaic SNVs from low-depth WGS data, because it supports low-depth samples, but DM does not call mosaic INDELs. I would like to detect mosaic...

Lumpyexpress produces zero INS and CNV

1

Hi. I ran lumpyexpress with my bam file using default options. But weirdly I got a vcf file that has only DEL, DUP, INV BND but no INS nor CNV....

Error in the nested 8-hicPipeline

2

Hi, I encountered an error in the very last step of `asm_sge/8-hicPipeline/final_contigs/8-hicPipeline/hic_scaff.sh` (not in `asm_sge/8-hicPipeline/hic_scaff.sh`! `asm_sge/8-hicPipeline/hic_scaff.sh` finished without error) hic_scaff.err ``` Traceback (most recent call last): File "/home/kogic/miniconda3/envs/verkko/lib/verkko/scripts/rdna_scaff.py", line 75,...