Input - Revision history

Albrecht at 08:57, 28 September 2021

2021-09-28T08:57:07Z

← Older revision		Revision as of 10:57, 28 September 2021
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	<pre>		<pre>
	./angsd -GL 1 -out genolike -doGlf 1 -doMajorMinor 1 -doMaf 2 -SNP_pval 2e-6 -bam bam.filelist -r 1:		./angsd -GL 1 -out genolike -doGlf 1 -doMajorMinor 1 -doMaf 2 -SNP_pval 1e-6 -bam bam.filelist -r 1:
	</pre>		</pre>

Thorfinn: /* Arguments */

2019-02-22T16:28:19Z

Arguments

← Older revision		Revision as of 18:28, 22 February 2019
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	</div>		</div>


	~~;-nInd [int]~~
	~~Number of individuals must be specified.~~
	~~;-fai [filename]~~
	~~The index to the reference genome.~~
	~~;-bpl [int]=33554432~~
	~~maximum bytes per line. Increase if the pileup has many individuals.~~
	;-nLines [int]=50		;-nLines [int]=50
	Number of lines to read at a time. Increasing this number will affect the RAM use.		Number of lines to read at a time. Increasing this number will affect the RAM use.


	===Tutorial===		===Tutorial===

Thorfinn: /* Example */

2019-02-22T16:27:54Z

Example

← Older revision		Revision as of 18:27, 22 February 2019
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	<pre>		<pre>
	/angsd -vcf-gl ~~file.vcf -fai hg19~~.fa.gz.~~fai~~ -~~nind 10~~ -domaf 4		angsd -vcf-gl ../smallBam/small2.bcf -domajorminor 1 -domaf 1
	</pre>		</pre>

Thorfinn: /* VCF files */

2019-02-22T16:25:03Z

VCF files

← Older revision		Revision as of 18:25, 22 February 2019
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	</pre>		</pre>

	=VCF files=		=BCF/VCF files=
	VCF file as input is now included but with some limitations. Only chr,pos~~,ref,alt~~ and ~~GP/GL~~ tags are being used, and we discard indels ~~and non diallelic sites.~~		BCF/VCF file as input is now included but with some limitations. Only chr,pos and PL tags are being used, and we discard indels.
	~~Furthermore you are required to include a fai file and the number of individuals~~.


	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">

Thorfinn: /* VCF files */

2019-02-22T16:24:14Z

VCF files

← Older revision		Revision as of 18:24, 22 February 2019
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	</pre>		</pre>

	==VCF files==		=VCF files=
	VCF file as input is now included but with some limitations. Only chr,pos,ref,alt and GP/GL tags are being used, and we discard indels and non diallelic sites.		VCF file as input is now included but with some limitations. Only chr,pos,ref,alt and GP/GL tags are being used, and we discard indels and non diallelic sites.
	Furthermore you are required to include a fai file and the number of individuals.		Furthermore you are required to include a fai file and the number of individuals.

Thorfinn: /* Sequence data (BAM/CRAM/mpileup) */

2019-02-22T16:23:59Z

Sequence data (BAM/CRAM/mpileup)

@@ Line 212: / Line 212: @@
 <pre>
 ./angsd -pileup sam.mpileup -nInd 10 -fai hg19.fa.gz.fai -domaf 1 -domajorminor 1 -gl 1
 </pre>

Thorfinn: /* VCF files */

2019-02-22T16:23:40Z

VCF files

@@ Line 311: / Line 311: @@
 </pre>
 Notice that -nInd and -fai needs to be supplied.
 =Genotype Probability Files=

Thorfinn: /* VCF files */

2019-02-22T16:23:23Z

VCF files

← Older revision		Revision as of 18:23, 22 February 2019
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	;-nLines [int]=50		;-nLines [int]=50
	Number of lines to read at a time. Increasing this number will affect the RAM use		Number of lines to read at a time. Increasing this number will affect the RAM use




	~~==VCF files==~~
	~~VCF file as input is now included but with some limitations. Only chr,pos,ref,alt and GP/GL tags are being used, and we discard indels and non diallelic sites.~~
	~~Furthermore you are required to include a fai file and the number of individuals.~~


	~~<div class="toccolours mw-collapsible mw-collapsed">~~
	~~./angsd -vcf-gp~~
	~~<pre class="mw-collapsible-content">~~
	~~-> angsd version: 0.910-20-g553b991 (htslib: 1.2.1-192-ge7e2b3d) build(Dec 4 2015 12:17:14)~~
	~~-> Analysis helpbox/synopsis information:~~
	~~-> Command:~~
	~~./angsd -vcf-gl -> Fri Dec 4 14:35:51 2015~~
	~~----------------~~
	~~multiReader.cpp:~~
	~~-nLines 50 (Number of lines to read)~~
	~~-bpl 33554432 (bytesPerLine)~~
	~~-beagle (null) (Beagle Filename (can be .gz))~~
	~~-vcf-GL (null) (vcf Filename (can be .gz))~~
	~~-vcf-GP (null) (vcf Filename (can be .gz))~~
	~~-glf (null) (glf Filename (can be .gz))~~
	~~-pileup (null) (pileup Filename (can be .gz))~~
	~~-intName 1 (Assume First column is chr_position)~~
	~~-isSim 0 (Simulated data assumes ancestral is A)~~
	~~-nInd 0 (Number of individuals)~~
	~~-minQ 13 (minimum base quality; only used in pileupreader)~~
	~~----------------~~
	~~multiReader.cpp:~~
	~~</pre>~~
	~~</div>~~

	NB The 4.2 version of the vcf specifiation clarifies that GP should be phred scaled post probs of the genotypes. But it seems that most software is using non-phred scale. So ANGSD uses the raw GP value. The GL tag is interpreted as log10.


	~~===Example===~~

	~~<pre>~~
	~~/angsd -vcf-gp file.vcf -fai hg19.fa.gz.fai -nind 10 -domaf 1~~
	~~</pre>~~

	~~===Arguments===~~

	~~;-vcf-gp [filename]~~
	~~name of the vcf file.~~
	~~<div class="toccolours mw-collapsible mw-collapsed">~~
	~~A vcf file~~
	~~<pre class="mw-collapsible-content">~~
	~~##fileformat=VCFv4.2(angsd version)~~
	~~##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">~~
	~~##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">~~
	~~##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">~~
	~~##FORMAT=<ID=GL,Number=G,Type=Float,Description="scaled Genotype Likelihoods (loglikeratios to the most likely (in log10))">~~
	~~#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind0 ind1~~
	~~1 14000873 . G A . PASS . GP:GL 0.000000,0.137003,0.862997:-15.128970,-1.505169,0.000000 0.716266,0.281975,0.001759:0.000000,-0.301034,-1.800000~~
	~~1 14001018 . T C . PASS . GP:GL 0.000000,0.081718,0.918282:-13.701492,-1.806203,0.000000 0.850652,0.149348,0.000000:0.000000,-0.602068,-5.699627~~
	~~1 14001867 . A G . PASS . GP:GL 0.000489,0.727550,0.271961:-3.600000,-0.301034,0.000000 0.914538,0.085462,0.000000:0.000000,-0.903101,-8.859124~~
	~~1 14002422 . A T . PASS . GP:GL 0.000000,0.291570,0.708430:-9.777061,-0.903101,0.000000 0.767047,0.232952,0.000001:0.000000,-0.602068,-5.499530~~
	~~1 14002474 . T C . PASS . GP:GL 0.995488,0.004512,0.000000:0.000000,-1.505169,-15.068561 0.965008,0.034992,0.000000:0.000000,-0.602068,-5.899399~~
	~~1 14003581 . C T . PASS . GP:GL 0.000000,0.674489,0.325510:-7.200000,-0.602068,0.000000 0.992516,0.007484,0.000000:0.000000,-1.806203,-13.447742~~
	~~1 14004623 . T C . PASS . GP:GL 0.000000,0.588345,0.411654:-6.999968,-0.602068,0.000000 0.989186,0.010814,0.000000:0.000000,-1.806203,-12.574310~~
	~~1 14007493 . A G . PASS . GP:GL 0.000013,0.541811,0.458176:-5.286503,-0.602068,0.000000 0.398233,0.422941,0.178826:-0.400000,-0.301034,0.000000~~
	~~1 14007558 . C T . PASS . GP:GL 0.000000,0.091908,0.908092:-15.524007,-1.505169,0.000000 0.284993,0.442044,0.272964:-0.400000,-0.301034,0.000000~~
	~~1 14007649 . G A . PASS . GP:GL 0.000000,0.638610,0.361390:-7.340205,-0.602068,0.000000 0.779442,0.220538,0.000020:0.000000,-0.301034,-3.500000~~
	~~1 14008734 . T A . PASS . GP:GL 0.000000,0.280425,0.719575:-13.909454,-1.204135,0.000000 0.757059,0.242817,0.000123:0.000000,-0.301034,-2.800000~~
	~~1 14009723 . G C . PASS . GP:GL 0.000345,0.744684,0.254971:-3.800000,-0.301034,0.000000 0.744903,0.255042,0.000055:0.000000,-0.301034,-3.200000~~
	~~1 14010597 . G A . PASS . GP:GL 0.000000,0.063511,0.936489:-17.446187,-1.806203,0.000000 0.684326,0.315309,0.000365:0.000000,-0.301034,-2.600000~~
	~~1 14010654 . T C . PASS . GP:GL 0.600538,0.348812,0.050650:0.000000,0.000000,0.000000 0.600538,0.348812,0.050650:0.000000,0.000000,0.000000~~
	~~</pre>~~
	~~</div>~~


	~~;-nInd [int]~~
	~~Number of individuals must be specified.~~
	~~;-fai [filename]~~
	~~The index to the reference genome.~~
	~~;-bpl [int]=33554432~~
	~~maximum bytes per line. Increase if the pileup has many individuals.~~
	~~;-nLines [int]=50~~
	~~Number of lines to read at a time. Increasing this number will affect the RAM use.~~

	~~===Tutorial===~~

	~~Create a VCF file using your favorate software or using angsd~~
	~~<pre>~~
	~~./angsd -b bam.filelist -dovcf 1 -gl 1 -dopost 1 -domajorminor 1 -domaf 1 -snp_pval 1e-6~~
	~~</pre>~~

	~~you can then use it as input to angsd if you have the GL info~~
	~~<pre>~~
	~~./angsd -vcf-gp angsdput.vcf.gz -nind 10 -fai hg19.fa.gz.fai -domaf 4~~
	~~</pre>~~

Thorfinn: /* -glf10_text */

2017-11-02T19:39:41Z

-glf10_text

← Older revision		Revision as of 21:39, 2 November 2017
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	==-glf10_text==		==-glf10_text==
			-glf10_text was added in commit: https://github.com/ANGSD/angsd/commit/46fc3edc181e80c4ad5e6bd644a64d23a5012e0e nov2 2017.
			This allows for reading files in the output format as -doglf 4.
			This is a simple text file with column 1 and column 2 being chromosome/scaffold and position. Then for each individual there are 10 logscaled genotype likelihoods in the order: AA,AC,AG,AT,CC,CG,CT,GG,GT,TT.
			Example runs are:
			First generate an example of this format:
			<pre>
			./angsd -gl 1 -doglf 4 -bam list -out first -domajorminor 1 -domaf 1
			</pre>

			This generates the file first.glf.gz. Which we can then use as input.
			Example here:
			<pre>
			./angsd -glf10_text first.glf.gz -nind 33 -domaf 1 -domajorminor 1 -fai fai.fai
			</pre>
			Notice that -nInd and -fai needs to be supplied.

	==VCF files==		==VCF files==

Thorfinn: /* VCF files */

2017-11-02T19:35:19Z

VCF files

← Older revision		Revision as of 21:35, 2 November 2017
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	./angsd -glf genolike.glf.gz -nInd 10 -fai hg19.fa.gz.fai -domaf 2 -domajorminor 1		./angsd -glf genolike.glf.gz -nInd 10 -fai hg19.fa.gz.fai -domaf 2 -domajorminor 1
	</pre>		</pre>

			==-glf10_text==

	==VCF files==		==VCF files==