Haploid calling - Revision history

Thorfinn: /* Major bug in version 0.911 (not in <0.911) */

2020-10-27T09:21:25Z

Major bug in version 0.911 (not in <0.911)

← Older revision		Revision as of 11:21, 27 October 2020
Line 1:		Line 1:
	Simple haploid output based on sampling or consensus. Latest github version of angsd has a small utility program in the misc folde that converts to plink output (tfam/tped).		Simple haploid output based on sampling or consensus. Latest github version of angsd has a small utility program in the misc folde that converts to plink output (tfam/tped).


	~~=Major bug in version 0.911 (not in <0.911)=~~
	~~Use the developmental version [https://github.com/ANGSD/angsd github]~~


Line 13:		Line 10:
	[sequence data]->[*.haplo.gz\|single base file{bg:blue}]		[sequence data]->[*.haplo.gz\|single base file{bg:blue}]
	</classdiagram>		</classdiagram>


	=Brief Overview=		=Brief Overview=

Thorfinn at 09:11, 10 August 2016

2016-08-10T09:11:11Z

← Older revision		Revision as of 11:11, 10 August 2016
Line 1:		Line 1:
	Simple haploid output based on sampling or consensus.		Simple haploid output based on sampling or consensus. Latest github version of angsd has a small utility program in the misc folde that converts to plink output (tfam/tped).


	=Major bug in version 0.911 (not in <0.911)=		=Major bug in version 0.911 (not in <0.911)=
	Use the developmental version [https://github.com/ANGSD/angsd github]		Use the developmental version [https://github.com/ANGSD/angsd github]

Albrecht: /* Output */

2016-03-14T08:33:43Z

Output

← Older revision		Revision as of 10:33, 14 March 2016
Line 86:		Line 86:
	columns are		columns are

	- chr chromosome		; chr
	- pos position		chromosome
	- major major allele (most common of the sampled alleles)		; pos
	- ind0 first individual - same order as in the input files		position
			; major
			major allele (most common of the sampled alleles)
			; ind0
			first individual - same order as in the input files

Albrecht: /* Output */

2016-03-14T08:33:01Z

Output

← Older revision		Revision as of 10:33, 14 March 2016
Line 84:		Line 84:
	1 14010748 A G N A G A A A		1 14010748 A G N A G A A A
	</pre>		</pre>
			columns are

			- chr chromosome
			- pos position
			- major major allele (most common of the sampled alleles)
			- ind0 first individual - same order as in the input files

Albrecht at 11:34, 13 March 2016

2016-03-13T11:34:49Z

← Older revision		Revision as of 13:34, 13 March 2016
Line 1:		Line 1:
	Simple haploid output based on sampling or consensus.		Simple haploid output based on sampling or consensus.
	Major bug in version 0.911 (not in <0.911). Use the developmental version [https://github.com/ANGSD/angsd github]		=Major bug in version 0.911 (not in <0.911)=
			Use the developmental version [https://github.com/ANGSD/angsd github]

Albrecht at 11:33, 13 March 2016

2016-03-13T11:33:44Z

← Older revision		Revision as of 13:33, 13 March 2016
Line 1:		Line 1:
	Simple haploid output based on sampling or consensus.		Simple haploid output based on sampling or consensus.
	~~This is available from versions >~~ 0.~~910 or from~~ the developmental version [https://github.com/ANGSD/angsd github]		Major bug in version 0.911 (not in <0.911). Use the developmental version [https://github.com/ANGSD/angsd github]

Albrecht at 09:17, 28 January 2016

2016-01-28T09:17:37Z

← Older revision		Revision as of 11:17, 28 January 2016
Line 1:		Line 1:
	Simple haploid output based on sampling or consensus.		Simple haploid output based on sampling or consensus.
			This is available from versions > 0.910 or from the developmental version [https://github.com/ANGSD/angsd github]


	__TOC__		__TOC__

Albrecht: /* Output */

2016-01-03T14:28:37Z

Output

← Older revision		Revision as of 16:28, 3 January 2016
Line 60:		Line 60:

	<pre>		<pre>
	1 ~~14094607~~ C C N N C C C T		chr pos major ind0 ind1 ind2 ind3 ind4 ind5 ind6
	1 ~~14094618 C C~~ N N C G ~~C N~~		1 14000170 C T T C N C C C
	1 ~~14094619~~ G ~~C N N~~ G N G G		1 14000202 A A N G A N N G
	~~1 14094628 C~~ G N ~~N N C N G~~		1 14000457 G G G G G G N A
	1 ~~14094784~~ G G G ~~T T N~~ G G		1 14000459 G G G G G A N N
	~~1 14095072 A~~ A N ~~A A A A C~~		1 14000774 G T G G G G G T
	~~1 14095751 C C C C C~~ N ~~T C~~		1 14002083 C G N C C C C C
	1 ~~14095773~~ G G G G G G N T		1 14002351 A A C C A C N A
	1 ~~14095992~~ C C ~~A N N~~ C A C		1 14002950 A T A A A T N T
	1 ~~14096030~~ C C C N A N ~~C N~~		1 14004832 G G G A G G A G
	1 ~~14096362~~ G T G G G G G G		1 14006543 G T G G G G G G
	1 ~~14096635~~ A T A A N A ~~N N~~		1 14006631 A C N A N A N A
	~~1 14096717 C C N C C C C N~~		1 14007068 G T T T G G G N
	1 ~~14097480 A A~~ G ~~A A A A A~~		1 14009284 A A C C C N A N
	~~1 14097899~~ T T T G ~~T T~~ G T		1 14009775 G G G G G C G C
	~~1 14098042~~ G T N ~~G T T G T~~		1 14009787 T T T G T G T T
	1 ~~14098127~~ A A N C A N ~~A A~~		1 14009791 A G G A G A G A
	1 ~~14098140~~ G G N G G G N G		1 14009794 A A A A N N A A
	~~1 14098148 C A N C C C N~~ C		1 14009800 A G A A G N G A
	1 ~~14098346~~ T T T T G T G G		1 14010748 A G N A G A A A
	1 ~~14098792 T T N T~~ A N T N
	1 ~~14099223~~ G G G ~~T G G~~ G G
	</pre>		</pre>

Albrecht: Created page with "Simple haploid output based on sampling or consensus. TOC [BAM files{bg:orange}]->[Sequence data|Random base;Consensus base] [sequence da..."

2016-01-03T14:27:53Z

Created page with "Simple haploid output based on sampling or consensus. __TOC__ <classdiagram type="dir:LR"> [BAM files{bg:orange}]->[Sequence data|Random base;Consensus base] [sequence da..."

New page

Simple haploid output based on sampling or consensus.

__TOC__

<classdiagram type="dir:LR">
[BAM files{bg:orange}]->[Sequence data|Random base;Consensus base]
[sequence data]->[*.haplo.gz|single base file{bg:blue}]
</classdiagram>

=Brief Overview=
<pre>
> ./angsd -doHaploCall
-> angsd version: 0.910-45-g2b2b4f0-dirty (htslib: 1.2.1-192-ge7e2b3d) build(Jan 3 2016 14:45:41)
-> Analysis helpbox/synopsis information:
-> Command:
./angsd -doHaploCall -> Sun Jan 3 15:18:15 2016
--------------
abcHaploCall.cpp:
-doHaploCall 0
(Sampling strategies)
0: no haploid calling
1: (Sample single base)
2: (Concensus base)
-doCounts 0 Must choose -doCount 1
Optional
-minMinor 0 Minimum observed minor alleles
-maxMis -1 Maximum missing bases (per site)

</pre>

This function outputs a base for each individual for each site

=Options=
;-doHaploCall [int]
1; sample a random base
2; most frequent base. Random base for ties
; -doCounts 1
use -doCounts 1 in order to count the bases at each sites after filters.
;-minMinor [int]
Minimum observed minor alleles; only prints sites with more than minMinor sampled alleles (across individuals).
; -maxMis [int]
maximum allowed missing alleles (accross individuals). -maxMis 0 means only sites without missing alleles are printed

=Output=
;*.haplo.gz
Output: Each line represents site. chromsome name (Column 1), position (Column 2), major allele (Column 3). One column for each individual with the sampled allele.

==Example==
Create a fasta file bases from a random samples of bases.

<pre>
./angsd -bam bam.filelist -dohaplocall 1 -doCounts 1 -r 1: -minMinor 1
</pre>

=Output=

<pre>
1 14094607 C C N N C C C T
1 14094618 C C N N C G C N
1 14094619 G C N N G N G G
1 14094628 C G N N N C N G
1 14094784 G G G T T N G G
1 14095072 A A N A A A A C
1 14095751 C C C C C N T C
1 14095773 G G G G G G N T
1 14095992 C C A N N C A C
1 14096030 C C C N A N C N
1 14096362 G T G G G G G G
1 14096635 A T A A N A N N
1 14096717 C C N C C C C N
1 14097480 A A G A A A A A
1 14097899 T T T G T T G T
1 14098042 G T N G T T G T
1 14098127 A A N C A N A A
1 14098140 G G N G G G N G
1 14098148 C A N C C C N C
1 14098346 T T T T G T G G
1 14098792 T T N T A N T N
1 14099223 G G G T G G G G
</pre>

Haploid calling - Revision history

Thorfinn: /* Major bug in version 0.911 (not in <0.911) */

Thorfinn at 09:11, 10 August 2016

Albrecht: /* Output */

Albrecht: /* Output */

Albrecht at 11:34, 13 March 2016

Albrecht at 11:33, 13 March 2016

Albrecht at 09:17, 28 January 2016

Albrecht: /* Output */

Albrecht: Created page with "Simple haploid output based on sampling or consensus. __TOC__ [BAM files{bg:orange}]->[Sequence data|Random base;Consensus base] [sequence da..."

Albrecht: Created page with "Simple haploid output based on sampling or consensus. TOC [BAM files{bg:orange}]->[Sequence data|Random base;Consensus base] [sequence da..."