Glcomparison - Revision history

Thorfinn at 15:44, 5 February 2016

2016-02-05T15:44:41Z

← Older revision		Revision as of 17:44, 5 February 2016
Line 63:		Line 63:

	aplot <- function(x,...){		aplot <- function(x,...){
	d<-~~exp~~(scan(x))		d<-(scan(x))
	p <- 1-d[1]-d[length(d)]		p <- 1-d[1]-d[length(d)]
	barplot(norm(d[-c(1,length(d))]),col=2,legend=paste0("var=",round(p*100,3)),...)		barplot(norm(d[-c(1,length(d))]),col=2,legend=paste0("var=",round(p*100,3)),...)

Thorfinn at 10:11, 12 August 2014

2014-08-12T10:11:04Z

← Older revision		Revision as of 12:11, 12 August 2014
Line 1:		Line 1:

			[[File:Glcomparison.png\|thumb]]
	For some analysis the choice of GL model will make a huge impact, this is shown in the example where we estimate the sfs using '''-GL 1''' and '''-GL 2''', for two list of BAM files downloaded from the 1000genomes project website. First list are 12 CEU samples from 2011, and second list are the same 12 CEU samples but from 2013.		For some analysis the choice of GL model will make a huge impact, this is shown in the example where we estimate the sfs using '''-GL 1''' and '''-GL 2''', for two list of BAM files downloaded from the 1000genomes project website. First list are 12 CEU samples from 2011, and second list are the same 12 CEU samples but from 2013.

Line 74:		Line 76:
	dev.off()		dev.off()
	</pre>		</pre>

	~~[[File:Glcomparison.png\|thumb]]~~

Thorfinn at 10:05, 12 August 2014

2014-08-12T10:05:51Z

← Older revision		Revision as of 12:05, 12 August 2014
Line 74:		Line 74:
	dev.off()		dev.off()
	</pre>		</pre>

			[[File:Glcomparison.png\|thumb]]

Thorfinn at 10:04, 12 August 2014

2014-08-12T10:04:30Z

@@ Line 51: / Line 51: @@
 realSFS res/old.list.gl1.saf 36 -P 24 >res/old.list.gl1.saf.ml
 realSFS res/old.list.gl2.saf 36 -P 24 >res/old.list.gl2.saf.ml
 </pre>

Thorfinn at 10:03, 12 August 2014

2014-08-12T10:03:08Z

@@ Line 41: / Line 41: @@
 NA11881.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam
 NA11992.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam
 </pre>

Thorfinn at 09:57, 12 August 2014

2014-08-12T09:57:02Z

@@ Line 8: / Line 8: @@
 angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/old.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
 angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/old.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
 </pre>

Thorfinn at 09:54, 12 August 2014

2014-08-12T09:54:07Z

← Older revision		Revision as of 11:54, 12 August 2014
Line 5:		Line 5:
	<pre>		<pre>
	angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/new.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6		angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/new.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
	~~/home/thorfinn/angsd/~~angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/new.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6		angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/new.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
	~~/home/thorfinn/angsd/~~angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/old.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6		angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/old.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
	~~/home/thorfinn/angsd/~~angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/old.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6		angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/old.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
	</pre>		</pre>

Thorfinn: Created page with "For some analysis the choice of GL model will make a huge impact, this is shown in the example where we estimate the sfs using '''-GL 1''' and '''-GL 2''', for two list of BAM..."

2014-08-12T09:53:40Z

Created page with "For some analysis the choice of GL model will make a huge impact, this is shown in the example where we estimate the sfs using '''-GL 1''' and '''-GL 2''', for two list of BAM..."

New page

For some analysis the choice of GL model will make a huge impact, this is shown in the example where we estimate the sfs using '''-GL 1''' and '''-GL 2''', for two list of BAM files downloaded from the 1000genomes project website. First list are 12 CEU samples from 2011, and second list are the same 12 CEU samples but from 2013.

Below are the commands used

<pre>
angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/new.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
/home/thorfinn/angsd/angsd -b new.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/new.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
/home/thorfinn/angsd/angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 1 -out res/old.list.gl1 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
/home/thorfinn/angsd/angsd -b old.list -minQ 20 -minMapQ 30 -isBed 1 -sites 1kg.accesible2.gz -GL 2 -out res/old.list.gl2 -doSaf 1 -r 1: -anc hg19ancNoChr.fa -P 6
</pre>