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Revision as of 01:27, 20 June 2014
, 01:27, 20 June 2014no edit summary
Set these values. If you used a different path for any of these, please update here. Also, be sure to specify your sample name instead of Sample_XXXXX
Set these values. If you used a different path for any of these, please update here. Also, be sure to specify your sample name instead of Sample_XXXXX
source /home/mktrost/seqshop-server/setup.txt
source /home/mktrost/seqshop/setup.2x.txt
export SAMPLE=Sample_XXXXX
export SAMPLE=Sample_XXXXX
export ALIGN_OUT=~/personal/output
export CHR20_OUT=~/personal/output.20
mkdir -p $CHR20_OUT
ALIGN_OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately
Verify that this does not give an error:
Verify that this does not give an error:
ls $OUT/bams/${SAMPLE}.recal.bam
ls $ALIGN_OUT/bams/${SAMPLE}.recal.bam
== Chromosome 20 ==
We want to add the 100 1000G chr20 BAMs to your bam list. Let's copy the original one into a new one so we can run other tests later.
cp $ALIGN_OUT/bam.index $CHR20_OUT/bam.20.index
Now add the chr20 BAMs to your new bam list:
cat $IN/chr20/bam.20.index >> $CHR20_OUT/bam.20.index
Verify you have 101 lines in your list:
wc -l $CHR20_OUT/bam.20.index
Update your gotcloud configuration file to indicate only chromosome 20 and point to the new list:
nedit ~/personal/gotcloud.2x.conf
Update OUT_DIR & BAM_INDEX to:
OUT_DIR = $(IN_DIR)/output.20
BAM_INDEX = $(OUT_DIR)/bam.20.index
Tell it you only want to process chromosome 20, by adding the following anywhere in the file:
CHRS = 20
Since it would take a while to run chrom 20 for 101 samples, I already ran the first step for the 100 1000G samples.
We will "trick" GotCloud into thinking you already ran them by copying them into your output directory.
cp -r $IN/chr20/glfs $CHR20_OUT/.
Now you are ready to run. Specify your chr20 bam list on the command line (or you could update BAM_INDEX in your conf file.
$GC/gotcloud snpcall --conf ~/personal/gotcloud.2x.conf --numjobs 1
=== GotCloud Configuration Updates ===
=== GotCloud Configuration Updates ===
