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Revision as of 12:39, 15 June 2014
, 12:39, 15 June 2014→Examining GotCloud SnpCall Output
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[[File:SvmFiltGL.png|550px]]
[[File:SvmFiltGL.png|550px]]
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=== 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.
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;Want an explanation of this command?
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* 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
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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?
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*Answer
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* Yes
** It should have scrolled and you should see filters like:
*** INDEL5;SVM
*** INDEL5
*** SVM
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