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need a simple background introduction

Prerequisites

Some tools are required,

python v2.7.14
samtools v1.7
cftools v1.7
htslib v1.7
netMHCpan v4.0

Example

use the supported files in example to run

• example/skcm/patients_missense_mutationl/TCGA.SKCM.mutect.4b7a5729-b83e-4837-9b61-a6002dce1c0a.DR-10.0.somatic.maf - download data from TCGA.
• example/skcm/patients_missense_mutationl/patients_id.txt - the records of patients' ID.
• example/skcm/patients_missense_mutationl/Homo_sapiens.GRCh38.pep.rename.fa - procced sequnce file.
• example/skcm/patients_missense_mutationl/HLA_list - the list of HLA-A,HLA-B,HLA-C unit.
• example/skcm/patients_missense_mutationl/submit_single.sh - change the header to fit your cluster.
• example/skcm/patients_missense_mutationl/get_fragments.py - to get the fragment sequnce.
• example/skcm/patients_missense_mutationl/get_amp_single.py - to make prediction.

cd example/skcm/patients_missense_mutationl
unzip TCGA.SKCM.mutect.4b7a5729-b83e-4837-9b61-a6002dce1c0a.DR-10.0.somatic.zip
cat TCGA.SKCM.mutect.4b7a5729-b83e-4837-9b61-a6002dce1c0a.DR-10.0.somatic.maf  | grep -v "^#" | grep Missense_Mutation | grep PASS|grep SNP| cut -f 1,5-13,55,56,68,111,116 > Missense_Mutation.PASS.txt
mkdir patients_missense_mutation
awk 'NR>1 {print "grep "$0" Missense_Mutation.PASS.txt > patients_missense_mutation/"$0".txt &"}' patients_id.txt > get_id.sh
chmod a+x get_id.sh
#get the file named by pation ID, the file look like 745c699b-8ecf-4653-b41f-6620f11bcf39.txt
./get_id.sh > get_id.log 2>&1 & 

cd patients_missense_mutation 
mkdir all wt mt 
#fragment sequnces will be genertsted in wt/ mt/ all/ resprectly
python get_fragments.py 

#prediction step
awk '{print "sbatch submit_single.sh "$0" >>all_HLA_job_ids"}' HLA_list > submit_HLA_jobs.sh
chmod a+x submit_HLA_jobs.sh
./submit_HLA_jobs.sh  > log  2>&1 & 

Notice: if the space is not enough in running prediction step, please split HLA_list file to some small files, such as "HLAa.list, HLAb.list, HLAc.list", and replace above "HLA_list" with them one by one.

Authors

• Yang Liu - University of Missouri, Columbia MO, USA
• Duolin Wang - University of Missouri, Columbia MO, USA
• Bowen Tang - University of Missouri, Columbia MO, USA
• Email - [email protected]
• Email - [email protected]
• Email - [email protected]

License

GNU v2.0