pipeline version: bwa59_b37_v4

Part I: getting B37 topstrand file converted

1. calling a script to update run summary file and create B37 topstrand if not yet created.

1. Script: /home/jl407/svnroot/bioinfoDev/jyli/topStrandRelated/modRunSmry.pl
2. Input (run_summary file owned by Ryan) i.e. exRealign_Summary_09.30.11.txt
3. Input log file: any_log.txt
4. Command: qsub /home/jl407/svnroot/bioinfoDev/jyli/topStrandRelated/modRunSmry.pl exRealign_Summary_09.30.11.txt B36ToB37_log.txt
5. Output:
a) An updated run_summary file is created/updated:
b) Build37 TopStrand files will be created,

Part II: getting the pipeline running
1) Taking a path for sample_info file (hard coded for now)
2) Change samtools version to 1.17

Testing batch mode run:

Step 1: Use /seqpipe02/ for this realignment project
Step 2: Create sample_info directory under /ALIGNMENT/
Step 3: Getting sample_info files set up: perl ../seqpipe01/SOFTWARE/alignment_scripts/sample_info_reAlign.pl ~/temp/realignSample /nfs/chgv/seqraw01/summaries/exRealign_Summary_08.17.11.txt

Step 4: Generating scripts:

ERROR “/nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/bwa59_b37_v1.pl” assumes sample_info file exist “/nfs/chgv/seqpipe01/ALIGNMENT/sample_info/bna007_info.txt”

perl /nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/submit_sample_jobs_meta.pl ~/temp/realignSample exome seqpipe02 bwa seqsata09 seqsata09 all high jl407 not 1 compute1.lsrc.duke.edu kit=37 6
Note: here 6 indicates to use bwa59_b37_v4

Step 3: Running pipeline:

perl /nfs/chgv/seqpipe01/SOFTWARE/alignment_scripts/submit_sample_jobs_meta.pl ~/temp/realignSample exome seqpipe02 all

Step 4: perl /nfs/seqsata01/ALIGNMENT/Scripts/copy_error_check_build37.pl sampleList BUILD37

Step 5: perl /nfs/seqsata01/ALIGNMENT/Scripts/check_copy_wrapper.pl sampleList genome|exome /alignmentDir/ BUILD37

Step 6: perl /nfs/seqsata01/ALIGNMENT/Scripts/alignment_stats_b37.pl sample_list exome seqsata09

FIXME

Now, since Latasha is helping out, well, it has a few errors:

1. /nfs/seqsata12/ALIGNMENT/BUILD37/EXOME was owned by Latasha, she has to change the permission
2. I own ” /nfs/sva01/SequenceAnalyses/Concordance/BUILD37/b37_exome_concordance.csv”, so her concordance check fails
Solution: for k in `cat shortList `; do echo $k; qsub /nfs/seqsata12/ALIGNMENT/BUILD37/EXOME/$k/Scripts/concordance.sh; done;

3. “bwa59_b37_v4.pl” has a bug, therefore symbolic link does NOT work.
Solution: for k in `cat shortList `; do echo $k; cd /nfs/seqsata12/ALIGNMENT/BUILD37/EXOME/$k/combined ; ln -s var_flt_vcf var_flt_vcf.vcf ; cd ../../ ; done;

There has been errors with concordance.sh script. I need to update it accordingly:

my $tempFile = $dir.”/”.$seqID.”_temp.txt”; #JYL modified 09/30/2011 for confusing name issue
my $tempFile = $dir.”/”.$gwasID.”_chipTemp.txt”;#JYL modified 09/30/2011 for confusing name issue
my $tempFile = $dir.”/”.$gwasID.”_chipTemp.txt”;#JYL modified 09/30/2011 for confusing name issue
my $tempFile = $dir.”/”.$gwasID.”_chipTemp.txt”;#JYL modified 09/30/2011 for confusing name issue