c2997108

Why scaffolds with 1 markers could be oriented?

1

Hi, When I used ALLMAPS with my data, I got the following summary.txt. ``` *** Summary for consensus map *** =============================================================================================== o Anchored Oriented Unplaced ----------------------------------------------------------------------------------------------- Markers (unique) 1,907 1,092...

I merged 93 samples with StringTie merge. Most of the isoforms were merged well, but when there is another isoform with another exon on the 5' side (in the example...

I built build/NA12878/test/GATKSVPipelineSingleSample.no_melt.json with scripts/inputs/build_default_inputs.sh. Next, I used the following cram file ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram and downloaded all gs:// files of GATKSVPipelineSingleSample.no_melt.json to my local server and modified the json file. GATKSVPipelineSingleSample.wdl...

I want to combine data using MakeCohortVcf after processing 500 samples multiple times in cohort mode

5

I was able to complete the processing of 500 samples in cohort mode using GATKSVPipelineBatch.wdl and would like to merge the results according to the instructions in the README. I...