Haploid calling

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).

flowchart LR
    n1["BAM files"]
    n2["Sequence data<br/>Random base<br/>Consensus base"]
    n3["*.haplo.gz<br/>single base file"]
    n1 --> n2
    n2 --> n3
    style n1 fill:#ffe0b2,stroke:#e65100
    style n3 fill:#bbdefb,stroke:#0d47a1

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Brief Overview

> ./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)

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.

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

Output

chr	pos	major	ind0	ind1	ind2	ind3	ind4	ind5	ind6
1	14000170	C	T	T	C	N	C	C	C
1	14000202	A	A	N	G	A	N	N	G
1	14000457	G	G	G	G	G	G	N	A
1	14000459	G	G	G	G	G	A	N	N
1	14000774	G	T	G	G	G	G	G	T
1	14002083	C	G	N	C	C	C	C	C
1	14002351	A	A	C	C	A	C	N	A
1	14002950	A	T	A	A	A	T	N	T
1	14004832	G	G	G	A	G	G	A	G
1	14006543	G	T	G	G	G	G	G	G
1	14006631	A	C	N	A	N	A	N	A
1	14007068	G	T	T	T	G	G	G	N
1	14009284	A	A	C	C	C	N	A	N
1	14009775	G	G	G	G	G	C	G	C
1	14009787	T	T	T	G	T	G	T	T
1	14009791	A	G	G	A	G	A	G	A
1	14009794	A	A	A	A	N	N	A	A
1	14009800	A	G	A	A	G	N	G	A
1	14010748	A	G	N	A	G	A	A	A

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