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, 12:39, 15 June 2014
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| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| [[File:SvmFiltGL.png|550px]] | | [[File:SvmFiltGL.png|550px]] |
| + | </div> |
| + | </div> |
| + | |
| + | |
| + | === Passing SNPs === |
| + | |
| + | Let's look at the file of just the pass sites: |
| + | less -S ${OUT}/split/chr22/chr22.filtered.PASS.vcf.gz |
| + | |
| + | * Scroll down: they all look like they <code>PASS</code> |
| + | |
| + | Let's check if they are all PASS. |
| + | zcat ${OUT}/split/chr22/chr22.filtered.PASS.vcf.gz |grep -v "^#"| cut -f 7| grep -v "PASS" |
| + | It will return nothing since there are no non-passing variants in this file. |
| + | <div class="mw-collapsible mw-collapsed" style="width:450px"> |
| + | ;Want an explanation of this command? |
| + | <div class="mw-collapsible-content"> |
| + | * zcat ...: uncompress the zipped VCF |
| + | * '|' : this takes the output of one command and sends it as input to the next |
| + | * grep -v "^#" : exclude any lines that start with "#" - headers |
| + | * cut -f 7 : extract the FILTER column (the 7th column) |
| + | * grep -v "PASS" : exclude any rows that have a "PASS" in the FILTER column |
| + | </div> |
| + | </div> |
| + | |
| + | Compare that to the filtered file we looked at before: |
| + | zcat ${OUT}/vcfs/chr22/chr22.filtered.vcf.gz |grep -v "^#"| cut -f 7| grep -v "PASS" |
| + | ;Do you see any filters? |
| + | <div class="mw-collapsible mw-collapsed" style="width:450px"> |
| + | *Answer |
| + | <div class="mw-collapsible-content"> |
| + | * Yes |
| + | ** It should have scrolled and you should see filters like: |
| + | *** INDEL5;SVM |
| + | *** INDEL5 |
| + | *** SVM |
| </div> | | </div> |
| </div> | | </div> |