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Revision as of 22:46, 16 June 2014
, 22:46, 16 June 2014Created page with "== What is vcf-summary? == <code>vcf-summary</code> is a utility included in GotCloud that helps evaluate the quality of SNP calls. Because GotCloud will automaticall..."
== What is vcf-summary? ==
<code>vcf-summary</code> is a utility included in [[GotCloud]] that helps evaluate the quality of SNP calls. Because [[GotCloud]] will automatically run <code>vcf-summary</code>, detailed instructions on the usage of the program is not currently documented.
== Example output from vcf-summary ==
If <code>OUT</code> is an environment variable, you may see output file from [[GotCloud ]] similar to the following example.
cat ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary
[[File:filterSum.png]]
The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.
== Rows of vcf-summary output has three sections ==
As shown in the example figure above, typical vcf-summary output primarily consists of the following three sections.
* In the first part, each SNP is counted only once, grouped by the contents of FILTER column.
* In the second part, each SNP may be counted multiple times, if the SNP failed multiple filters (e.g. INDEL5 filter and SVM filter).
* In the last part, each SNP is counted only once, grouped by SNPs with "PASS" in the FILTER column versus everything else.
In addition, multi-allelic or duplicated SNPs are counted separately at the very bottom.
<code>vcf-summary</code> is a utility included in [[GotCloud]] that helps evaluate the quality of SNP calls. Because [[GotCloud]] will automatically run <code>vcf-summary</code>, detailed instructions on the usage of the program is not currently documented.
== Example output from vcf-summary ==
If <code>OUT</code> is an environment variable, you may see output file from [[GotCloud ]] similar to the following example.
cat ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary
[[File:filterSum.png]]
The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.
== Rows of vcf-summary output has three sections ==
As shown in the example figure above, typical vcf-summary output primarily consists of the following three sections.
* In the first part, each SNP is counted only once, grouped by the contents of FILTER column.
* In the second part, each SNP may be counted multiple times, if the SNP failed multiple filters (e.g. INDEL5 filter and SVM filter).
* In the last part, each SNP is counted only once, grouped by SNPs with "PASS" in the FILTER column versus everything else.
In addition, multi-allelic or duplicated SNPs are counted separately at the very bottom.
