Understanding vcf-summary output - Revision history

Mktrost: /* Example output from vcf-summary */

2014-11-24T02:31:59Z

Example output from vcf-summary

← Older revision		Revision as of 22:31, 23 November 2014
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	cat ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary		cat ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary

	[[File:filterSumNew.png]]		[[File:filterSumNew.png\|700px]]

	The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.		The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.

Mktrost: /* Example output from vcf-summary */

2014-11-24T02:31:38Z

Example output from vcf-summary

← Older revision		Revision as of 22:31, 23 November 2014
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	cat ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary		cat ${OUT}/vcfs/chr22/chr22.filtered.sites.vcf.summary

	[[File:~~filterSum~~.png]]		[[File:filterSumNew.png]]

	The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.		The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.

Hmkang: /* Rows of vcf-summary output has three sections */

2014-06-17T03:30:24Z

Rows of vcf-summary output has three sections

← Older revision		Revision as of 23:30, 16 June 2014
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	The example above is obtained from the results of [[GotCloud]] within a very small (1Mb) region in chr22 across ~60 1000 Genomes samples.		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 ==		== Rows of vcf-summary output consist of three sections ==

	As shown in the example figure above, typical vcf-summary output primarily consists of the following three sections.		As shown in the example figure above, typical vcf-summary output primarily consists of the following three sections.

Hmkang: /* What should we expect from good SNP call sets? */

2014-06-17T03:29:43Z

What should we expect from good SNP call sets?

← Older revision		Revision as of 23:29, 16 June 2014
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	* Because of natural selection, in exomes, we expect higher Ts/Tv in known SNPs than novel SNPs. This is because novel SNPs are more likely to be non-synonymous SNPs than synonymous SNPs. Please refer to [[SNP_Call_Set_Properties]] for additional information.		* Because of natural selection, in exomes, we expect higher Ts/Tv in known SNPs than novel SNPs. This is because novel SNPs are more likely to be non-synonymous SNPs than synonymous SNPs. Please refer to [[SNP_Call_Set_Properties]] for additional information.
	* '''%dbSNP''' should be usually higher for '''PASS''' categories than others, indicating that known SNPs are more likely to pass filters. However, because dbSNP also contain false positive variants, we don't necessarily expect that '''%dbSNP''' go to zero even if the filtering works perfectly.		* '''%dbSNP''' should be usually higher for '''PASS''' categories than others, indicating that known SNPs are more likely to pass filters. However, because dbSNP also contain false positive variants, we don't necessarily expect that '''%dbSNP''' go to zero even if the filtering works perfectly.
	* Because HM3 consist of common SNPs, this number should be high when the sample size is large. Typically, if the sample contains only Europeans, the expected values of '''%HM3 sens''' are around 90%. If the sample contains African ancestry, the number will be close to 95% of higher.		* Because HM3 consist of common SNPs, this number should be high when the sample size is large. Typically, if the sample contains only Europeans, the expected values of '''%HM3 sens''' are around 90%. If the sample contains African ancestry, the number will be close to 95% of higher.
	* Note that some callers uses the expected difference between Ts and Tv in their calling model as prior. In that case, Ts/Tv could be biased by the prior, and Ts/Tv may not be a good indicator of SNP qualities.		* Note that some callers uses the expected difference between Ts and Tv in their calling model as prior. In that case, Ts/Tv could be biased by the prior, and Ts/Tv may not be a good indicator of SNP qualities.

Hmkang at 03:29, 17 June 2014

2014-06-17T03:29:14Z

← Older revision		Revision as of 23:29, 16 June 2014
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	In addition, multi-allelic or duplicated SNPs are counted separately at the very bottom.		In addition, multi-allelic or duplicated SNPs are counted separately at the very bottom.

			== Understanding the columns of vcf-summary output ==

			vcf-summary output can be a little bit dense to digest at the first time, but contains useful information about the quality of SNP calls.

			First, define transitions and transversions..
			* '''Transition''' (Ts or Ti) refers to the bi-allelic SNPs where two alleles are A <-> G or C <-> T. In true SNPs, transitions more frequently occurs than transversions.
			* '''Transversion''' (Tv) refers to the bi-allelic SNPs that are not transitions.

			Each column of vcf-summary output shows..

			* '''FILTER''' shows the groups of SNPs represented by FILTER columns in the VCF file. See previous section to know how SNPs are grouped.
			* '''#SNPs''' shows the total number of SNPs that belong to each FILTER category.
			* '''#dbSNPs''' shows the number of SNPs that appear in the dbSNP. The version of dbSNP can be different based on the GotCloud version (e.g. 129, 135, 137)
			* '''%dbSNPs''' are simply [#dbSNPs] / [#SNPs], indicating the fraction of variants ''known'' by dbSNP. The rest of them will be considered as ''novel''
			* '''%CpG Known''' are the fraction of known (in dbSNP) SNPs that are located at CpG sites, which are enriched for transitions.
			* '''%CpG Novel''' are the fraction of novel (not in dbSNP) SNPs that are located at CpG sites, which are enriched for transitions.
			* '''Known Ts/Tv''' represents Ts/Tv ratio among known (in dbSNP) SNPs.
			* '''Novel Ts/Tv''' represents Ts/Tv ratio among novel (not in dbSNP) SNPs.
			* '''nCpG-K Ts/Tv''' represents Ts/Tv ratio among known (in dbSNPs) SNPs, when only focusing on non-CpG sites. Ts/Tv becomes more stable when excluding CpG sites.
			* '''nCpG-N Ts/Tv''' represents Ts/Tv ratio among novel (in dbSNPs) SNPs, when only focusing on non-CpG sites.
			* '''%HM3 sens''' indicate the percent of HapMap3 SNPs rediscovered among all HapMap SNPs ( [# HapMap3-overlapping SNPs] / [# all HapMap 3 SNPs] )
			* '''%HM3/SNP''' indicate the percent of HapMap3 SNPs among all SNPs in the call set ( [# HapMap3-overlapping SNPs] / [# all SNPs in the call set] )

			== What should we expect from good SNP call sets? ==

			If the SNP filtering was effective, you will expect the following properties in "PASS" category, but not in the other categories.

			* Metrics between '''Known''' and '''Novel''' categories should be similar. This indicates that novel SNPs show as good qualities as known SNPs, which are enriched for true variants.
			* Expected '''Ts/Tv''' values for whole genome call set are around 2.2. '''non-CpG Ts/Tv''' are usually ranged around 1.8
			* For exome call sets, Ts/Tv are expected to be higher (around 3). Synonymous SNPs will have higher Ts/Tv (around 5.5) than non-synonymous SNPs (around 2.2).
			* Because of natural selection, in exomes, we expect higher Ts/Tv in known SNPs than novel SNPs. This is because novel SNPs are more likely to be non-synonymous SNPs than synonymous SNPs. Please refer to [[SNP_Call_Set_Properties]] for additional information.
			* '''%dbSNP''' should be usually higher for '''PASS''' categories than others, indicating that known SNPs are more likely to pass filters. However, because dbSNP also contain false positive variants, we don't necessarily expect that '''%dbSNP''' go to zero even if the filtering works perfectly.
			* Because HM3 consist of common SNPs, this number should be high when the sample size is large. Typically, if the sample contains only Europeans, the expected values of '''%HM3 sens''' are around 90%. If the sample contains African ancestry, the number will be close to 95% of higher.
			* Note that some callers uses the expected difference between Ts and Tv in their calling model as prior. In that case, Ts/Tv could be biased by the prior, and Ts/Tv may not be a good indicator of SNP qualities.

Hmkang: Created page with "== What is vcf-summary? == `vcf-summary` is a utility included in GotCloud that helps evaluate the quality of SNP calls. Because GotCloud will automaticall..."

2014-06-17T02:46:29Z

Created 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..."

New page

== 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.

Understanding vcf-summary output - Revision history

Mktrost: /* Example output from vcf-summary */

Mktrost: /* Example output from vcf-summary */

Hmkang: /* Rows of vcf-summary output has three sections */

Hmkang: /* What should we expect from good SNP call sets? */

Hmkang at 03:29, 17 June 2014

Hmkang: Created page with "== What is vcf-summary? == vcf-summary is a utility included in GotCloud that helps evaluate the quality of SNP calls. Because GotCloud will automaticall..."

Hmkang: Created page with "== What is vcf-summary? == `vcf-summary` is a utility included in GotCloud that helps evaluate the quality of SNP calls. Because GotCloud will automaticall..."