Difference between revisions of "SeqShop: Calling Your Own Genome, June 2014"
Line 45: | Line 45: | ||
$GC/gotcloud snpcall --conf ~/personal/gotcloud.2x.conf --numjobs 1 | $GC/gotcloud snpcall --conf ~/personal/gotcloud.2x.conf --numjobs 1 | ||
− | == | + | == Exome == |
− | To speed things up, | + | To speed things up, I extracted only exome regions from 100 1000g low coverage BAMs. |
− | + | ||
+ | Let's create a new bam info file with your BAM combined with those BAMs. | ||
+ | cp $ALIGN_OUT/bam.index $EXOME_OUT/bam.exome.index | ||
+ | |||
+ | Now add the exome BAMs to your new bam list: | ||
+ | cat $IN/exome/bam.exome.index >> $EXOME_OUT/bam.exome.index | ||
+ | |||
+ | Verify you have 101 lines in your list: | ||
+ | wc -l $EXOME_OUT/bam.exome.index | ||
+ | |||
+ | Update your gotcloud configuration file to indicate exomes and point to the new list: | ||
+ | nedit ~/personal/gotcloud.2x.conf | ||
+ | |||
+ | Remember, we need to update the GotCloud Configuration to do this. | ||
Locate your gotcloud.2x.conf (probably at: ~/personal/gotcloud.2x.conf) and open it in your favorite editor: | Locate your gotcloud.2x.conf (probably at: ~/personal/gotcloud.2x.conf) and open it in your favorite editor: | ||
Line 61: | Line 74: | ||
WRITE_TARGET_LOCI = TRUE | WRITE_TARGET_LOCI = TRUE | ||
TARGET_DIR = target | TARGET_DIR = target | ||
+ | |||
+ | Update OUT_DIR & BAM_INDEX to: | ||
+ | OUT_DIR = $(IN_DIR)/output.exome | ||
+ | BAM_INDEX = $(OUT_DIR)/bam.exome.index | ||
+ | |||
+ | Remove CHRS = 20 | ||
== Run == | == Run == |
Revision as of 01:31, 20 June 2014
Login to the seqshop-server Linux Machine
This section will appear redundantly in each session. If you are already logged in or know how to log in to the server, please skip this section
- Login to the windows machine
- The username/password for the Windows machine should be written on the right-hand monitor
- Start xming so you can open external windows on our Linux machine
- Start->Enter "Xming" in the search and select "Xming" from the program list
- Nothing will happen, but Xming was started.
- Open putty
- Start->Enter "putty" in the search and select "PuTTY" from the program list
- Configure PuTTY in the PuTTY Configuration window
- Host Name:
seqshop-server.sph.umich.edu
- Setup to allow you to open external windows:
- In the left pannel: Connection->SSH->X11
- Add a check mark in the box next to
Enable X11 forwarding
- Click
Open
- If it prompts about a key, click
OK
- Enter your provided username & password as provided
You should now be logged into a terminal on the seqshop-server and be able to access the test files.
- If you need another terminal, repeat from step 3.
Login to the seqshop Machine
So you can each run multiple jobs at once, we will have you run on 4 different machines within our seqshop setup.
- You can only access these machines after logging onto seqshop-server
3 users logon to:
ssh -X seqshop1
3 users logon to:
ssh -X seqshop2
2 users logon to:
ssh -X seqshop3
2 users logon to:
ssh -X seqshop4
Setup
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/setup.2x.txt 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:
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
Exome
To speed things up, I extracted only exome regions from 100 1000g low coverage BAMs.
Let's create a new bam info file with your BAM combined with those BAMs.
cp $ALIGN_OUT/bam.index $EXOME_OUT/bam.exome.index
Now add the exome BAMs to your new bam list:
cat $IN/exome/bam.exome.index >> $EXOME_OUT/bam.exome.index
Verify you have 101 lines in your list:
wc -l $EXOME_OUT/bam.exome.index
Update your gotcloud configuration file to indicate exomes and point to the new list:
nedit ~/personal/gotcloud.2x.conf
Remember, we need to update the GotCloud Configuration to do this.
Locate your gotcloud.2x.conf (probably at: ~/personal/gotcloud.2x.conf) and open it in your favorite editor:
nedit ~/personal/gotcloud.2x.conf
Add
# Specify the path to the regions we want to call UNIFORM_TARGET_BED = $(REF_DIR)/20130108.exome.targets.nochr.bed # We do not want any off target bases OFFSET_OFF_TARGET = 0 WRITE_TARGET_LOCI = TRUE TARGET_DIR = target
Update OUT_DIR & BAM_INDEX to:
OUT_DIR = $(IN_DIR)/output.exome BAM_INDEX = $(OUT_DIR)/bam.exome.index
Remove CHRS = 20
Run
Set CHR = 1 2
cp -r /home/mktrost/seqshop/inputs/glfs personal/output/.
cp personal/output/bam.index personal/output/bam.exome.index
cat /home/mktrost/seqshop/inputs/20130502.gotcloud.low_coverage.100.index >> personal/output/bam.exome.index
wc -l personal/output/bam.exome.index
cp /home/mktrost/seqshop/inputs/gotcloud.exome.conf personal/.
Update the conf ...your home.
/home/mktrost/seqshop/gotcloud/gotcloud snpcall --conf personal/gotcloud.exome.conf