SNP calling - Revision history

Albrecht at 08:59, 28 September 2021

2021-09-28T08:59:02Z

← Older revision		Revision as of 10:59, 28 September 2021
Line 10:		Line 10:

	===example===		===example===
	In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the ~~samtools~~ method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and only keep those sites that have a p-value less than 1e-6 of for being variable.		In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the GATK method (-GL 2), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and only keep those sites that have a p-value less than 1e-6 of for being variable.

	<pre>		<pre>
	./angsd -bam bam.filelist -GL 1 -out outfile -doMaf 2 -SNP_pval 1e-6 -doMajorMinor 1		./angsd -bam bam.filelist -GL 2 -out outfile -doMaf 2 -SNP_pval 1e-6 -doMajorMinor 1
	</pre>		</pre>

Albrecht at 16:54, 5 March 2014

2014-03-05T16:54:47Z

← Older revision		Revision as of 18:54, 5 March 2014
Line 10:		Line 10:

	===example===		===example===
	In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the samtools method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and only keep those sites that have a p-value of 1e-6 for being variable.		In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the samtools method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and only keep those sites that have a p-value less than 1e-6 of for being variable.

	<pre>		<pre>
Line 17:		Line 17:

	===output===		===output===
	the results are given in the file outfile.mafs:		the results are given in the file outfile.mafs.gz:
	<pre>		<pre>
	chromo position major minor ~~knownEM pK~~-EM nInd		chromo position major minor unknownEM pu-EM nInd
	1 ~~14008260~~ C A 0.~~000001~~ -0.~~000074 32~~		1 14000873 G A 0.282476 0.000000e+00 10
	1 ~~14008261~~ A C 0.~~000000~~ -~~0.000051 31~~		1 14001018 T C 0.259890 7.494005e-14 9
	1 ~~14008262~~ G T 0.~~000001~~ -~~0.000099 32~~		1 14001867 A G 0.272099 6.361578e-14 10
	1 ~~14008263~~ C A 0.~~000001~~ -0.~~000093 32~~		1 14002422 A T 0.377890 0.000000e+00 9
	1 ~~14008264~~ A T 0.~~000010~~ -~~0.000574 32~~		1 14003581 C T 0.194393 5.551115e-16 9
	1 ~~14008265~~ T C 0.~~000001~~ -~~0.000144 31~~		1 14004623 T C 0.259172 2.424727e-13 10
	1 ~~14008266~~ G A 0.~~000000~~ -~~0.000049 31~~		1 14007493 A G 0.297176 5.114086e-07 9
	1 ~~14008267~~ G A 0.~~000001~~ -0.~~000100 31~~		1 14007558 C T 0.381770 0.000000e+00 8
	1 ~~14008268~~ G A 0.~~000001~~ -~~0.000081 30~~		1 14007649 G A 0.220547 1.054967e-11 9
	1 ~~14008269~~ G A 0.~~168397~~ ~~191~~.~~962068 31~~		1 14008734 T A 0.242852 0.000000e+00 10
	1 ~~14008270~~ G A 0.~~000001~~ -~~0.000075 31~~		1 14009723 G C 0.255063 2.470836e-07 10
	1 ~~14008271~~ A C 0.~~000001~~ -0.~~000109 31~~		1 14010597 G A 0.315430 0.000000e+00 10
	1 ~~14008272~~ A C 0.~~000001~~ -0.~~000081 29~~		1 14010851 C A 0.276936 0.000000e+00 10
	1 ~~14008273~~ A C 0.~~000002~~ -0.~~000156 30~~		1 14012240 C T 0.297956 0.000000e+00 10
	</pre>		</pre>
	The ~~colums~~ are the chromosome, the position, the major allele, the minor allele, the minor allele estimate, the ~~likelihood ratio statistic~~ and the number of individuals with information~~. In this example one site has a high likelihood ratio statistic~~.		The columns are the chromosome, the position, the major allele, the minor allele, the minor allele estimate, the allele frequency, the p-value and the number of individuals with information.

Albrecht at 18:04, 26 February 2014

2014-02-26T18:04:01Z

← Older revision		Revision as of 20:04, 26 February 2014
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	==Likelihood ratio test==		==Likelihood ratio test==
	SNPs are called based on their allele frequencies. If a site has a minor allele frequency significantly different from 0 a site i called as polymorphic. The MAF estimate(s) given by -doMaf (see [[Allele_Frequency_estimation]]), will be used for a like ratio test by using a chi-square distribution with ~~1df~~ for -doMaf 1 and ~~3df for~~ -doMaf 3.		SNPs are called based on their allele frequencies. If a site has a minor allele frequency significantly different from 0 a site is called as polymorphic. The MAF estimate(s) given by -doMaf (see [[Allele_Frequency_estimation]]), will be used for a like ratio test by using a chi-square distribution with one degree of freedom for -doMaf 1 and -doMaf 2.

	===options===		===options===

Thorfinn: /* example */

2014-01-16T00:49:39Z

example

← Older revision		Revision as of 02:49, 16 January 2014
Line 10:		Line 10:

	===example===		===example===
	In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the samtools method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and ~~calculates the likelihood ratio statistic (~~-~~doSNP 1)~~		In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the samtools method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and only keep those sites that have a p-value of 1e-6 for being variable.

	<pre>		<pre>

Thorfinn: /* example */

2014-01-16T00:49:01Z

example

← Older revision		Revision as of 02:49, 16 January 2014
Line 13:		Line 13:

	<pre>		<pre>
	./angsd -bam bam.filelist -GL 1 -out outfile -doMaf 2 -~~doSNP 1~~ -doMajorMinor 1		./angsd -bam bam.filelist -GL 1 -out outfile -doMaf 2 -SNP_pval 1e-6 -doMajorMinor 1
	</pre>		</pre>

Thorfinn: /* Likelihood ratio test */

2014-01-16T00:48:44Z

Likelihood ratio test

← Older revision		Revision as of 02:48, 16 January 2014
Line 2:		Line 2:

	==Likelihood ratio test==		==Likelihood ratio test==
	~~; -doSNP 1~~		SNPs are called based on their allele frequencies. If a site has a minor allele frequency significantly different from 0 a site i called as polymorphic. The MAF estimate(s) given by -doMaf (see [[Allele_Frequency_estimation]]), will be used for a like ratio test by using a chi-square distribution with 1df for -doMaf 1 and 3df for -doMaf 3.
	SNPs are called based on their allele frequencies. If a site has a minor allele frequency significantly different from 0 a site i called as polymorphic. The MAF estimate(s) given by -doMaf (see [[Allele_Frequency_estimation]]), will be used for a like ratio test and -~~2log(likelihood ratio) is the output~~.

	===options===		===options===
	; -~~minLrt~~ [float]		; -SNP_pval [float]
	~~default 0.~~ The ~~minimum likelihood ratio statistic used i further analysis and in the output. -minLrt 24 would only print site with a high likelihood ratio statistic corresonding to a~~ p-value ~~of approximately <math> 10^{-6}</math>~~		The p-value used for calling snaps.
	see [[Allele_Frequency_estimation]] for additional options		see [[Allele_Frequency_estimation]] for additional options

Albrecht at 13:27, 21 September 2012

2012-09-21T13:27:20Z

← Older revision		Revision as of 15:27, 21 September 2012
Line 1:		Line 1:
	==SNP Calling==		=SNP Calling=

	===Likelihood ratio test===		==Likelihood ratio test==
	~~supply~~ -doSNP 1		; -doSNP 1
	~~Then the~~ MAF estimate(s) given by -doMaf ~~INT~~, will be used for a like ratio test		SNPs are called based on their allele frequencies. If a site has a minor allele frequency significantly different from 0 a site i called as polymorphic. The MAF estimate(s) given by -doMaf (see [[Allele_Frequency_estimation]]), will be used for a like ratio test and -2log(likelihood ratio) is the output.

			===options===
			; -minLrt [float]
			default 0. The minimum likelihood ratio statistic used i further analysis and in the output. -minLrt 24 would only print site with a high likelihood ratio statistic corresonding to a p-value of approximately <math> 10^{-6}</math>
			see [[Allele_Frequency_estimation]] for additional options

			===example===
			In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the samtools method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and calculates the likelihood ratio statistic (-doSNP 1)

			<pre>
			./angsd -bam bam.filelist -GL 1 -out outfile -doMaf 2 -doSNP 1 -doMajorMinor 1
			</pre>

			===output===
			the results are given in the file outfile.mafs:
	<pre>		<pre>
	chromo position major minor knownEM pK-EM nInd		chromo position major minor knownEM pK-EM nInd
	~~21 9719770 T~~ A 0.~~000009~~ -0.~~000018~~ 1		1 14008260 C A 0.000001 -0.000074 32
	~~21 9719771~~ T A 0.000001 -0.~~000003~~ 1		1 14008261 A C 0.000000 -0.000051 31
	~~21 9719772~~ C A 0.000001 -0.~~000003~~ 1		1 14008262 G T 0.000001 -0.000099 32
	~~21 9719773 T~~ A 0.~~000002~~ -0.~~000010~~ 2		1 14008263 C A 0.000001 -0.000093 32
	21 ~~9719774~~ G A 0.~~000002~~ -0.~~000010~~ 2		1 14008264 A T 0.000010 -0.000574 32
	~~21 9719775~~ A C 0.~~000004~~ -0.~~000022~~ 2		1 14008265 T C 0.000001 -0.000144 31
	~~21 9719776 G~~ A 0.~~000002~~ -0.~~000010~~ 2		1 14008266 G A 0.000000 -0.000049 31
	~~21 9719777~~ A C 0.000002 -0.~~000013~~ 2		1 14008267 G A 0.000001 -0.000100 31
			1 14008268 G A 0.000001 -0.000081 30
			1 14008269 G A 0.168397 191.962068 31
			1 14008270 G A 0.000001 -0.000075 31
			1 14008271 A C 0.000001 -0.000109 31
			1 14008272 A C 0.000001 -0.000081 29
			1 14008273 A C 0.000002 -0.000156 30
	</pre>		</pre>
			The colums are the chromosome, the position, the major allele, the minor allele, the minor allele estimate, the likelihood ratio statistic and the number of individuals with information. In this example one site has a high likelihood ratio statistic.

Albrecht: Created page with "==SNP Calling== ===Likelihood ratio test=== supply -doSNP 1 Then the MAF estimate(s) given by -doMaf INT, will be used for a like ratio test

 chromo  position        ma..."

2012-06-18T14:18:50Z

Created page with "==SNP Calling== ===Likelihood ratio test=== supply -doSNP 1 Then the MAF estimate(s) given by -doMaf INT, will be used for a like ratio test <pre> chromo position ma..."

New page

==SNP Calling==

===Likelihood ratio test===
supply -doSNP 1
Then the MAF estimate(s) given by -doMaf INT, will be used for a like ratio test

<pre>
chromo position major minor knownEM pK-EM nInd
21 9719770 T A 0.000009 -0.000018 1
21 9719771 T A 0.000001 -0.000003 1
21 9719772 C A 0.000001 -0.000003 1
21 9719773 T A 0.000002 -0.000010 2
21 9719774 G A 0.000002 -0.000010 2
21 9719775 A C 0.000004 -0.000022 2
21 9719776 G A 0.000002 -0.000010 2
21 9719777 A C 0.000002 -0.000013 2

</pre>