Introduction - Revision history

Thorfinn at 17:13, 23 October 2012

2012-10-23T17:13:41Z

← Older revision		Revision as of 19:13, 23 October 2012
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			===Whats on this page===
			This page will contain som random examples.

			==Examples==



	Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8.		Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8.

Thorfinn at 07:15, 23 October 2012

2012-10-23T07:15:38Z

← Older revision		Revision as of 09:15, 23 October 2012
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	./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1		./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1
	</pre>		</pre>
	This is using the SAMtools model for calculating genotype likelihoods (see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models). Without the '-doGlf' parameter the genotype likelihoods will solely be estimated but will not be dumped. Therefore we also supply the '-doGlf 1' which will dump the genotype likelihoods as binary see [[Genotype_likelihoods_from_alignments#output_genotype_likelihoods \|Gl outputs]].		This is using the SAMtools model for calculating genotype likelihoods (see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models). Without the '-doGlf' parameter the genotype likelihoods will solely be estimated but will not be dumped. Therefore we also supply the '-doGlf 1' which will dump the genotype likelihoods as binary see [[Genotype_likelihoods_from_alignments#output_genotype_likelihoods \|GL outputs]].

Thorfinn at 07:15, 23 October 2012

2012-10-23T07:15:23Z

← Older revision		Revision as of 09:15, 23 October 2012
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	./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1		./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1
	</pre>		</pre>
	This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models. Without the '-doGlf' parameter the genotype likelihoods will solely be estimated but will not be dumped. Therefore we also supply the ;'-doGlf 1' which will dump the genotype likelihoods as binary see [[Genotype_likelihoods_from_alignments#output_genotype_likelihoods \|Gl outputs]].		This is using the SAMtools model for calculating genotype likelihoods (see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models). Without the '-doGlf' parameter the genotype likelihoods will solely be estimated but will not be dumped. Therefore we also supply the '-doGlf 1' which will dump the genotype likelihoods as binary see [[Genotype_likelihoods_from_alignments#output_genotype_likelihoods \|Gl outputs]].

Thorfinn at 07:14, 23 October 2012

2012-10-23T07:14:47Z

← Older revision		Revision as of 09:14, 23 October 2012
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	<pre>		<pre>
	./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results		./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results -doGlf 1
	</pre>		</pre>
	This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models.		This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models. Without the '-doGlf' parameter the genotype likelihoods will solely be estimated but will not be dumped. Therefore we also supply the ;'-doGlf 1' which will dump the genotype likelihoods as binary see [[Genotype_likelihoods_from_alignments#output_genotype_likelihoods \|Gl outputs]].

Thorfinn at 07:08, 23 October 2012

2012-10-23T07:08:54Z

← Older revision		Revision as of 09:08, 23 October 2012
Line 4:		Line 4:
	./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results		./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results
	</pre>		</pre>
	This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods]] for other models.		This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods from alignments \| genotype likelihoods]] for other models.

Thorfinn at 07:07, 23 October 2012

2012-10-23T07:07:34Z

← Older revision		Revision as of 09:07, 23 October 2012
Line 4:		Line 4:
	./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results		./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results
	</pre>		</pre>
	This is using the SAMtools model for calculating genotype likelihoods see [Genotype likelihoods] for other models.		This is using the SAMtools model for calculating genotype likelihoods see [[Genotype likelihoods]] for other models.

Thorfinn at 07:07, 23 October 2012

2012-10-23T07:07:00Z

← Older revision		Revision as of 09:07, 23 October 2012
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	<pre>		<pre>
	./angsd -bam list.txt -GL 1 -r chr8:12500000		./angsd -bam list.txt -GL 1 -r chr8:12500000 -out results
	</pre>		</pre>
			This is using the SAMtools model for calculating genotype likelihoods see [Genotype likelihoods] for other models.

Thorfinn: Created page with "Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8.

 ./angsd -bam list.txt -GL 1 -r ..."

2012-10-23T07:05:22Z

Created page with "Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8. <pre> ./angsd -bam list.txt -GL 1 -r ..."

New page

Assuming you have a list of bamfiles in in file: 'list.txt' and you want the genotype likelihoods for position 12500000 on chromosome 8.

<pre>
./angsd -bam list.txt -GL 1 -r chr8:12500000
</pre>