Line 28: |
Line 28: |
| == Examining GotCloud Indel Input files == | | == Examining GotCloud Indel Input files == |
| The GotCloud Indel caller takes the same inputs as GotCloud snpcall. | | The GotCloud Indel caller takes the same inputs as GotCloud snpcall. |
| + | * BAMs->INDELs rather than BAMs->SNPs |
| | | |
| If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]] | | If you want a reminder, of what they look like, here is a link to the previous tutorial : [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#Examining_GotCloud_SnpCall_Input_files|GotCloud SnpCall Input Files]] |
Line 33: |
Line 34: |
| == Running GotCloud Indel == | | == Running GotCloud Indel == |
| ${GC}/gotcloud indel --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 | | ${GC}/gotcloud indel --conf ${IN}/gotcloud.conf --numjobs 2 --region 22:36000000-37000000 |
| + | * --numjobs tells GotCloud how many jobs to run in parallel |
| + | ** Depends on your system |
| + | * --region 22:36000000-37000000 |
| + | ** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions |
| + | |
| + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| + | Curious if it started running properly? Check out this screenshot: |
| + | <div class="mw-collapsible-content"> |
| + | [[File:indelStart.png|550px]] |
| + | </div> |
| + | </div> |
| + | This should take about 4-5 minutes to run. |
| + | * It should end with a line like: <code>Commands finished in 289 secs with no errors reported</code> |
| + | |
| + | If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off. |
| + | |
| + | |
| + | == Examining GotCloud indel Ouptut == |
| + | Let's look at the output directory: |
| + | ls ${OUT} |
| + | |
| + | ;Do you see any new files or directories? |
| + | <div class="mw-collapsible mw-collapsed" style="width:350px"> |
| + | * View Annotated Screenshot: |
| + | <div class="mw-collapsible-content"> |
| + | [[File:indelOut.png|500px]] |
| + | </div> |
| + | </div> |
| + | |
| + | Let's look at the <code>final</code> directory: |
| + | ls ${OUT}/final |
| + | Just a <code>chr22</code> directory, so look inside of there: |
| + | ls ${OUT}/vcfs/chr22 |
| + | ;Can you identify the final indel VCF? |
| + | <div class="mw-collapsible mw-collapsed" style="width:350px"> |
| + | * Answer & annotated directory listing: |
| + | <div class="mw-collapsible-content"> |
| + | <ul> |
| + | <li>all.genotypes.vcf.gz</li> |
| + | </ul> |
| + | [[File:indelOutFinal.png|600px]] |
| + | </div> |
| + | </div> |