https://github.com/kennethabarr/HumanChimp
Raw File
Tip revision: 1722b3484d1120384c910bef13bffd6a6cd6179a authored by kennethabarr on 02 July 2021, 18:06:58 UTC
first commit
Tip revision: 1722b34
config.yaml
#Snakemake configuration file

#This contains the setup for a human/chimp run on 10x

#directory with additional scripts
ken_scripts: /project2/gilad/kenneth/Pipelines/Scripts/

#logfile
dir_log: log/

#individuals
humans: NA19160.variant2,NA18511.variant2,NA18858.variant2,SCM-6.variant,SCM-7.variant,SCM-8.variant,SCM-9.variant,SCM-10.variant,SCM-12.variant,SCM-13.variant
chimps: SCM-2,SCM-3,SCM-4
  
#Genome fa
human_fa: /project2/gilad/kenneth/References/human/genome/hg38.fa
chimp_fa: /project2/gilad/kenneth/References/chimp/genome/panTro6.fa
 
#Genome index for STAR aligner
human_genome_index: /project2/gilad/kenneth/References/human/STARindex/ens98_hg38_full_99/
chimp_genome_index: /project2/gilad/kenneth/References/chimp/STARindex/full_chimp_inhuman/

#whitelist 
whitelist: /project2/gilad/kenneth/References/whitelists/whitelist.v3.txt

#demuxlet files
human_vcf: /project2/gilad/kenneth/References/human/vcfs/human.HC_YRI.hg38.exons.vcf
chimp_vcf: /project2/gilad/kenneth/References/chimp/vcfs/output.pt6.exons.vcf

# script locations
popscle: /project2/gilad/kenneth/software/popscle/bin/popscle
samtools: /project2/gilad/kenneth/software/samtools-1.10/samtools

#it wont use my conda python so for some reason i need to link it to the python bin
python: /scratch/midway2/barr/miniconda3/envs/chromium/bin/python

#transcript file
human_txn_file: /project2/gilad/kenneth/References/human/GTF/ens98.filtered.gtf
chimp_txn_file: /project2/gilad/kenneth/References/chimp/GTF/gencode.transmap.filtered.withM.gtf

# cell barcode UMI Configuration
barcode: "CCCCCCCCCCCCCCCCNNNNNNNNNN"
back to top