Monthly Archives: December 2011

Status: b57mod008 –> need re-run b57mod010 –> need re-run b57mod011 –> test ad hoc run, done and bam file copied b57mod016 –> test ad hoc run, done and bam file copied b57mod030 –> copying, done and bam file copied b57mod013 … Continue reading →

Using “b57mod016″ as test run: Step 1: create a “temp” subfolder, and move all .sam/.bam file into the “temp” folder Step 2: modified “/nfs/chgv/seqpipe01/ALIGNMENT/samples/b57mod016/Scripts/SAMPE/sampe_1_RG.sh” Step 3: Two ways: 1. Get RG information added at sampe step, and run merge with … Continue reading →

Per email from David: Jianying & Min With the new plans in our annotation approach Joe may wish to consider application of Annovar to variants called for Macaque, my guess is that is the sensible approach. I haven’t looked through … Continue reading →

Per Kevin’s email: I realize it’s an n of 1, but that should give us a good idea. also, you just aligned 5 b57 samples using the new build 37 pipeline. Instead of transferring new data why don’t you align … Continue reading →

Since we are supporting build37, this is the first batch of “exome annotation” with SVA. Although SVA will soon phase out, we can’t afford not having something in place to support “temporary” for build37 alignment results. Here is an email … Continue reading →

This is command calling the error checking on lsrc, we need to make it work: perl /nfs/seqsata01/ALIGNMENT/Scripts/copy_error_check_build37.pl sample_in_process genome /nfs/seqsata13/ /nfs/seqsata13 The script exists under subversion control: /home/jl407/svnroot/bioinfoDev/jyli/utils/copy_error_check_build37.pl Using meta0001 genome realignment as an example to test it out perl … Continue reading →

Pipeline doc: BWA_Alignment_Documentation_basics Variant call SOP: CHGV_SOP_Alignment_Variant_Calling_033111[1]