Keep 10X notes, reports, results, (small) datasets etc. as you wish. Basically instead of dumping everything in the Google doc, feel free to dump it in here.
| Description | Path | Cluster |
|---|---|---|
| NA12878 WGS from 10X-wfu | /data/cephfs/punim0010/data/External/Reference/NA12878-10x-2018/wfu |
Spartan |
| NA12878 WGS from 10X-wg1 re-run | /data/cephfs/punim0010/data/External/Reference/NA12878-10x-2018/NA12878_WGS_v2 |
Spartan |
| NA12878 WGS from 10X-wfu re-run | /g/data3/gx8/projects/Hsu_10X_WGS/NA12878-10X-WFU |
Raijin |
| NA12878 WES from 10X-wes | /data/cephfs/punim0010/data/External/Reference/NA12878-10x-2018/WES |
Spartan |
| LongRanger + References | /data/projects/punim0010/opt/ |
Spartan |
| GRCh37 non-decoy Reference | /data/cephfs/punim0010/extras/10x/refdata-GRCh37 |
Spartan |
| Name | Description | Notes |
|---|---|---|
| bxtools | light-weight tools for 10X data | has conda package |
| longranger | 10X official pipeline for WGS/WES read alignment, SNP/Indel/SV calling and phasing | has docker |
| HapCut2 | haplotype assembly | - |
| EMA | align 10X reads | has conda package |
| ZoomX | somatic SV calling | on bitbucket |
| bazam | extract paired reads in FASTQ format from coordinate sorted BAM files | Simon Sadedin at 10X symposium |
| gemtools | phase SVs in 10X reads | Hanlee Ji at 10X symposium |