...
| Code Block |
|---|
| language | bash |
|---|
| title | suggested direcotry directory set up |
|---|
|
cds
cp -r $BI/gva_course/structural_variation/data sv_tutorial
cd sv_tutorial |
...
| Warning |
|---|
| title | Do not run on head node |
|---|
|
Many of the commands past this point are computationally intensive. You should run them through an idev shell or by qsub. We recommend idev for the tutorial, but you could also qsub any command that takes more than a few seconds to complete. | Code Block |
|---|
| title | Example command to start an idev shell |
|---|
| idev -m 60 -q development -A CCBB"UT-2015-05-18" |
|
| Code Block |
|---|
bowtie2-build NC_012967.1.fasta NC_012967.1
bowtie2 -p 12 -X 5000 --rf -x NC_012967.1 -1 61FTVAAXX_2_1.fastq -2 61FTVAAXX_2_2.fastq -S 61FTVAAXX.sam |
...
SVDetect demonstrates a common strategy in some programs with complex input where instead of including a lot of options on the command line, it reads in a simple text file that sets all of the required options. Lets look at how to create a configuration file:
| Note |
|---|
You'll need to substitute your own paths for /full/path/to/61FTVAAXX.ab.sam and /full/path/to/NC_012967.1.lengths on lines 7 and 8 below. |
| Code Block |
|---|
| title | Create the file svdetect.conf with this text |
|---|
| linenumbers | true |
|---|
|
<general>
input_format=sam
sv_type=all
mates_orientation=RF
read1_length=35
read2_length=35
mates_file=/full/path/to/61FTVAAXX.ab.sam
cmap_file=/full/path/to/NC_012967.1.lengths
num_threads=1
</general>
<detection>
split_mate_file=0
window_size=2000
step_length=1000
</detection>
<filtering>
split_link_file=0
nb_pairs_threshold=3
strand_filtering=1
</filtering>
<bed>
<colorcode>
255,0,0=1,4
0,255,0=5,10
0,0,255=11,100000
</colorcode>
</bed>
|
| Note |
|---|
You'll need to substitute your own paths for /full/path/to/61FTVAAXX.ab.sam and /full/path/to/NC_012967.1.lengths.
You also need to create a tab-delimited file of chromosome lengths. Use the tab key rather than writing out <tab>!!
...
You'll want to submit the first two commands to the TACC queue or do them in an idev shell. They take a while.Consult Consult the manual for a full description of what these commands and options are doing while the commands are running.
| Code Block |
|---|
| title | Commands to run SNVDetect |
|---|
|
SVDetect linking -conf svdetect.conf
SVDetect filtering -conf svdetect.conf
SVDetect links2SV -conf svdetect.conf
|
Take a look at the resulting file: 61FTVAAXX.ab.sam.links.filtered.sv.txt.
We've highlighted a few lines below:
| Code Block |
|---|
chr_type SV_type BAL_type chromosome1 start1-end1 average_dist chromosome2 start2-end2 nb_pairs score_strand_filtering score_order_filtering score_insert_size_filtering final_score breakpoint1_start1-end1 breakpoint2_start2-end2
...
INTRA NORMAL_SENSE - chrNC_012967 599566-601025 - chrNC_012967 663036-664898 430 100% - - 1 - -
...
INTRA NORMAL_SENSE - chrNC_012967 3-2025 - chrNC_012967 4627019-4628998 288 100% - - 1 - -
...
INTRA REVERSE_SENSE - chrNC_012967 16999-19033 - chrNC_012967 2775082-2777014 274 100% - - 1 - -
|
| Expand |
|---|
| title | Any idea what sorts of mutations produced these three structural variants? |
|---|
|
...
| Expand |
|---|
|
1. This is a tandem head-to-tail duplication of the region from approximately 600000 to 663000.
2. This is just the origin of the circular chromosome, connecting its end to the beginning!
3. This is a big chromosomal inversion mediated by recombination between repeated IS elements in the genome. It would not have been detected if the insert size of the library wasn't > ~1,500 bp! ... Many of the others are due to new insertions of transposable elements. |
...