Understanding vcf-summary output

What is vcf-summary?

vcf-summary is a utility included in GotCloud that helps evaluate the quality of SNP calls. Because GotCloud will automatically run vcf-summary, detailed instructions on the usage of the program is not currently documented.

Example output from vcf-summary

If OUT 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

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.