Thetas,Tajima,Neutrality tests - Revision history

Thorfinn: /* Full command list for below examples */

2020-08-27T12:40:14Z

Full command list for below examples

← Older revision		Revision as of 14:40, 27 August 2020
Line 18:		Line 18:
	<pre>		<pre>
	./angsd -bam bam.filelist -doSaf 1 -anc chimpHg19.fa -GL 1 -P 24 -out out		./angsd -bam bam.filelist -doSaf 1 -anc chimpHg19.fa -GL 1 -P 24 -out out
			#for unfolded
	./misc/realSFS out.saf.idx -P 24 > out.sfs		./misc/realSFS out.saf.idx -P 24 > out.sfs
	~~#use -fold 1 in the above command if you dont have ancestral state.~~
	./misc/realSFS saf2theta out.saf.idx -outname out -sfs out.sfs		./misc/realSFS saf2theta out.saf.idx -outname out -sfs out.sfs
			#for folded
			./misc/realSFS out.saf.idx -P 24 -fold 1 > out.sfs
			./misc/realSFS saf2theta out.saf.idx -outname out -sfs out.sfs -fold 1
	#Estimate for every Chromosome/scaffold		#Estimate for every Chromosome/scaffold
	./misc/thetaStat do_stat out.thetas.idx		./misc/thetaStat do_stat out.thetas.idx

Thorfinn: /* Step 1: Finding a 'global estimate' of the SFS */

2020-04-01T11:06:34Z

Step 1: Finding a 'global estimate' of the SFS

← Older revision		Revision as of 13:06, 1 April 2020
Line 59:		Line 59:
	<pre>		<pre>
	./misc/realSFS out.saf.idx -P 24 > out.sfs		./misc/realSFS out.saf.idx -P 24 > out.sfs
			</pre>
			Or if want to calculate the folded spectrum.
			<pre>
			./misc/realSFS out.saf.idx -P 24 -fold 1 > out.sfs
	</pre>		</pre>

Thorfinn: /* Full command list for below examples */

2020-04-01T11:05:30Z

Full command list for below examples

← Older revision		Revision as of 13:05, 1 April 2020
Line 15:		Line 15:
	# Calculate neutrality tests statistics. Output is a '''.thetas.idx.pestPG file.		# Calculate neutrality tests statistics. Output is a '''.thetas.idx.pestPG file.
	==Full command list for below examples==		==Full command list for below examples==
	Here is the chain of commands required to do estimate the thetas, and perform neutrality test statistics. These different commands are described in great detail in the following '''step 1,... step 3b''' sub sections.		Here is the chain of commands required to do estimate the thetas, and perform neutrality test statistics. These different commands are described in great detail in the following '''step 1,... step 3b''' sub sections. If you do not have the ancestral state you can simply use the assembly you have mapped agains, but remember to add -fold 1 in the 'realSFS' and 'realSFS sf2theta' step.
	<pre>		<pre>
	./angsd -bam bam.filelist -doSaf 1 -anc chimpHg19.fa -GL 1 -P 24 -out out		./angsd -bam bam.filelist -doSaf 1 -anc chimpHg19.fa -GL 1 -P 24 -out out

Thorfinn: /* Full command list for below examples */

2020-04-01T11:03:25Z

Full command list for below examples

← Older revision		Revision as of 13:03, 1 April 2020
Line 19:		Line 19:
	./angsd -bam bam.filelist -doSaf 1 -anc chimpHg19.fa -GL 1 -P 24 -out out		./angsd -bam bam.filelist -doSaf 1 -anc chimpHg19.fa -GL 1 -P 24 -out out
	./misc/realSFS out.saf.idx -P 24 > out.sfs		./misc/realSFS out.saf.idx -P 24 > out.sfs
	./~~angsd -bam bam~~.~~filelist~~ -~~out~~ out -~~doThetas 1 -doSaf 1 -pest~~ out.sfs ~~-anc chimpHg19.fa -GL 1~~		#use -fold 1 in the above command if you dont have ancestral state.
			./misc/realSFS saf2theta out.saf.idx -outname out -sfs out.sfs
	#Estimate for every Chromosome/scaffold		#Estimate for every Chromosome/scaffold
	./misc/thetaStat do_stat out.thetas.idx		./misc/thetaStat do_stat out.thetas.idx

Thorfinn: /* Unknown ancestral state (folded sfs) */

2020-04-01T10:56:52Z

Unknown ancestral state (folded sfs)

@@ Line 200: / Line 200: @@
 =Unknown ancestral state (folded sfs)=
 If you don't have the ancestral states, you can still calculate the Watterson and Tajima theta, which means you can perform the Tajima's D neutrality test statistic. But this requires you to use the folded sfs. The output files will have the same format, but only the thetaW and thetaD, and tajimas D is meaningful.
-Below is an example based on the earlier example where we now base our analysis on the folded spectrum. Notice the -fold 1
+There was previously an example below that showed how to perform this analysis. This information has now been added to the examples above (notice the -fold 1) step in realSFS.
 =Citation=
 [[Korneliussen2013]]

Thorfinn: /* Step 2: Calculate the thetas for each site */

2020-04-01T10:52:30Z

Step 2: Calculate the thetas for each site

← Older revision		Revision as of 12:52, 1 April 2020
Line 70:		Line 70:
	==Step 2: Calculate the thetas for each site==		==Step 2: Calculate the thetas for each site==
	<pre>		<pre>
	.~~/angsd -bam bam~~.~~filelist~~ -~~out out -doThetas 1 -doSaf 1 -pest~~ out.sfs -~~anc chimpHg19.fa -GL 1~~		realSFS saf2theta out.saf.idx -sfs out.sfs -outname out
	</pre>		</pre>
	The output from the above command are two files out.thetas.gz and out.thetas.idx. A formal description of these files can be found in the doc/formats.pdf in the angsd package. It is possible to extract the logscale persite thetas using the ./thetaStat print program.		The output from the above command are two files out.thetas.gz and out.thetas.idx. A formal description of these files can be found in the doc/formats.pdf in the angsd package. It is possible to extract the logscale persite thetas using the ./thetaStat print program.

Thorfinn: /* Example Output */

2017-05-29T19:53:16Z

Example Output

← Older revision		Revision as of 21:53, 29 May 2017
Line 131:		Line 131:
	=Example Output=		=Example Output=
	<pre>		<pre>
	- Output in the ./thetaStat ~~pritn~~ thetas.idx are the log scaled per site estimates of the thetas		- Output in the ./thetaStat print thetas.idx are the log scaled per site estimates of the thetas
	- Output in the pestPG file are the sum of the per site estimates for a region		- Output in the pestPG file are the sum of the per site estimates for a region
	</pre>		</pre>

Thorfinn: /* .thetas.gz.pestPG */

2017-02-08T16:59:14Z

.thetas.gz.pestPG

← Older revision		Revision as of 18:59, 8 February 2017
Line 163:		Line 163:
	;7. ThetaL		;7. ThetaL

	==.thetas.gz.pestPG==		==.thetas.idx.pestPG==
	The .pestPG file is a 14 column file (tab seperated). The first column contains information about the region. The second and third column is the reference name and the center of the window.		The .pestPG file is a 14 column file (tab seperated). The first column contains information about the region. The second and third column is the reference name and the center of the window.

Thorfinn: /* Example */

2017-02-08T16:58:46Z

Example

← Older revision		Revision as of 18:58, 8 February 2017
Line 7:		Line 7:
	For performing the ML method, you should the use the [[SFS Estimation]] method and define the region af interest.		For performing the ML method, you should the use the [[SFS Estimation]] method and define the region af interest.

	=Example=		=Quick Example=
	Below is a chain of commands used for caculating statistics. These are based on the test files that can be dowloaded on the [[Quick Start ]] page.		Below is a chain of commands used for caculating statistics. These are based on the test files that can be dowloaded on the [[Quick Start ]] page.

	Its a 3 step procedure		Its a 3 step procedure
	# Estimate an site frequency spectrum. Output is '''out.sfs''' file. This is what is being used as the '''-pest ''' argument in step2.		# Estimate an site frequency spectrum. Output is '''out.sfs''' file. This is what is being used as the '''-pest ''' argument in step2.
	# Calculate per-site thetas. Output is a '''.thetas.idx/.thetas.gz''' files.		# Calculate per-site thetas. Output is a '''.thetas.idx/.thetas.gz''' files. This contains the binary persite estimates of the thetas.
	# Calculate neutrality tests statistics. Output is a '''.thetas.idx.pestPG file.		# Calculate neutrality tests statistics. Output is a '''.thetas.idx.pestPG file.
	==Full command list for below examples==		==Full command list for below examples==

Thorfinn: /* ./thetaStat print angsdput.thetas.gz */

2017-02-08T16:57:28Z

./thetaStat print angsdput.thetas.gz

← Older revision		Revision as of 18:57, 8 February 2017
Line 134:		Line 134:
	- Output in the pestPG file are the sum of the per site estimates for a region		- Output in the pestPG file are the sum of the per site estimates for a region
	</pre>		</pre>
	==./thetaStat print angsdput.thetas.gz==		==./thetaStat print angsdput.thetas.idx==
	<pre>		<pre>
	#Chromo Pos Watterson Pairwise thetaSingleton thetaH thetaL		#Chromo Pos Watterson Pairwise thetaSingleton thetaH thetaL