ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.936/0.937 on github), see Change_log for changes, and download it here.

Vcf

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Newer versions of angsd (master 27april2015) supports basic vcf output. This will only include gl and gp tags which can be useful for certain external programs

Supply

-doVcf 1

Which is simply a wrapper around -gl -dopost -domajorminor -domaf.


Example

A full example commandline is given below:

 ./angsd -b list.list -dovcf 1 -gl 1 -dopost 1 -domajorminor 1 -domaf 1 -snp_pval 1e-6

Output files

This will generate a vcf file called angsdput.vcf.gz

angsdput.vcf.gz

##FORMAT=<ID=GL,Number=G,Type=Float,Description="scaled Genotype Likelihoods (these are really llh eventhough they sum to one)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ind0	ind1	ind2	ind3	ind4	ind5	ind6	ind7	ind8	ind9	ind10	ind11	ind12	ind13	ind14	ind15	ind16	ind17	ind18	ind19	ind20	ind21	ind22	ind23	ind24	ind25	ind26	ind27	ind28	ind29	ind30	ind31	ind32
1	14000202	.	G	A	.	PASS	.	GL:GP	0.013409,0.986591,0.000001:0.009959,0.990038,0.000003	0.532745,0.394297,0.072957:0.333333,0.333333,0.333333	0.532745,0.394297,0.072957:0.333333,0.333333,0.333333	0.729804,0.270070,0.000126:0.666110,0.333052,0.000839	0.532745,0.394297,0.072957:0.333333,0.333333,0.333333	0.013409,0.986589,0.000003:0.009959,0.990026,0.000015	0.843814,0.156129,0.000057:0.799685,0.199918,0.000397	0.003405,0.996582,0.000013:0.002523,0.997410,0.000068	0.915318,0.084679,0.000003:0.888870,0.111106,0.000025	0.843862,0.156138,0.000000:0.800003,0.199997,0.000000	0.001243,0.728985,0.269772:0.000420,0.333191,0.666388	0.955789,0.044211,0.000000:0.941178,0.058822,0.000000	0.843860,0.156137,0.000003:0.799987,0.199993,0.000020	0.000001,0.999999,0.000000:0.000001,0.999999,0.000000	0.824856,0.152621,0.022523:0.689947,0.172484,0.137569	0.701963,0.259767,0.038270:0.526842,0.263419,0.209740	0.532745,0.394297,0.072957:0.333333,0.333333,0.333333	0.004272,0.995611,0.000117:0.003164,0.996204,0.000632	0.532745,0.394297,0.072957:0.333333,0.333333,0.333333	0.021392,0.791754,0.186854:0.008712,0.435643,0.555645	0.843681,0.156104,0.000215:0.798816,0.199700,0.001484	0.729804,0.270070,0.000126:0.666110,0.333052,0.000839	0.002698,0.996374,0.000928:0.001990,0.993012,0.004997	0.977395,0.022605,0.000000:0.969698,0.030302,0.000000	0.532745,0.394297,0.072957:0.333333,0.333333,0.333333	0.002152,0.997847,0.000002:0.001593,0.998397,0.000010	0.915213,0.084669,0.000118:0.888149,0.111016,0.000835	0.032903,0.965645,0.001452:0.024405,0.967730,0.007865	0.000006,0.999994,0.000000:0.000005,0.999995,0.000000	0.701963,0.259767,0.038270:0.526842,0.263419,0.209740	0.843846,0.156135,0.000019:0.799896,0.199971,0.000133	0.907127,0.083921,0.008952:0.835380,0.104420,0.060201	0.332066,0.644735,0.023200:0.241926,0.634652,0.123421
1	14000873	.	G	A	.	PASS	.	GL:GP	0.000000,0.124151,0.875849:0.000000,0.030302,0.969698	0.692531,0.305335,0.002134:0.659698,0.329846,0.010456	0.900720,0.099279,0.000000:0.888891,0.111109,0.000000	0.993158,0.006842,0.000000:0.992249,0.007751,0.000000	0.999140,0.000860,0.000000:0.999024,0.000976,0.000000	0.000091,0.994381,0.005528:0.000078,0.975325,0.024596	0.900720,0.099279,0.000000:0.888891,0.111109,0.000000	0.819369,0.180627,0.000004:0.799988,0.199993,0.000018	0.000000,0.124151,0.875849:0.000000,0.030302,0.969698	0.693938,0.305955,0.000107:0.666316,0.333155,0.000529	0.986410,0.013590,0.000000:0.984616,0.015384,0.000000	0.693919,0.305947,0.000135:0.666224,0.333109,0.000666	0.007101,0.988541,0.004358:0.006172,0.974344,0.019484	0.000000,1.000000,0.000000:0.000000,1.000000,0.000000	0.030451,0.672875,0.296674:0.013127,0.328956,0.657917	0.973184,0.026816,0.000000:0.969698,0.030302,0.000000	0.973184,0.026816,0.000000:0.969698,0.030302,0.000000	0.993158,0.006842,0.000000:0.992249,0.007751,0.000000	0.004535,0.995465,0.000000:0.004001,0.995998,0.000000	0.000395,0.693734,0.305871:0.000167,0.333276,0.666557	0.900720,0.099279,0.000000:0.888891,0.111109,0.000000	0.693965,0.305967,0.000068:0.666446,0.333220,0.000334	0.947768,0.052232,0.000000:0.941178,0.058822,0.000000	0.000000,0.220881,0.779119:0.000000,0.058822,0.941178	0.900720,0.099279,0.000000:0.888891,0.111109,0.000000	0.000000,0.017410,0.982590:0.000000,0.003891,0.996109	0.000046,0.999954,0.000000:0.000040,0.999960,0.000000	0.000001,0.999999,0.000000:0.000001,0.999999,0.000000	0.947768,0.052232,0.000000:0.941178,0.058822,0.000000	0.310721,0.689279,0.000000:0.284441,0.715559,0.000000	0.900720,0.099279,0.000000:0.888891,0.111109,0.000000	0.973184,0.026816,0.000000:0.969698,0.030302,0.000000	0.000992,0.693320,0.305688:0.000420,0.333191,0.666388
1	14001018	.	T	C	.	PASS	.	GL:GP	0.000000,0.069163,0.930837:0.000000,0.015384,0.984616	0.826258,0.173742,0.000000:0.800002,0.199997,0.000002	0.159620,0.840380,0.000000:0.137752,0.862248,0.000000	0.950058,0.049942,0.000000:0.941178,0.058822,0.000000	0.904865,0.095135,0.000000:0.888891,0.111109,0.000000	0.826258,0.173742,0.000000:0.800003,0.199997,0.000000	0.495544,0.416810,0.087646:0.333333,0.333333,0.333333	0.993472,0.006528,0.000000:0.992249,0.007751,0.000000	0.001055,0.703204,0.295741:0.000420,0.333191,0.666388	0.703933,0.296042,0.000025:0.666580,0.333287,0.000133	0.826258,0.173742,0.000000:0.800003,0.199997,0.000000	0.703933,0.296042,0.000025:0.666580,0.333287,0.000133	0.000420,0.703651,0.295929:0.000167,0.333276,0.666557	0.000008,0.999992,0.000000:0.000006,0.999994,0.000000	0.085860,0.913986,0.000153:0.073175,0.926086,0.000739	0.904865,0.095135,0.000000:0.888891,0.111109,0.000000	0.495544,0.416810,0.087646:0.333333,0.333333,0.333333	0.993472,0.006528,0.000000:0.992249,0.007751,0.000000	0.703731,0.295957,0.000313:0.665554,0.332774,0.001672	0.000007,0.543141,0.456852:0.000002,0.199997,0.800001	0.904865,0.095135,0.000000:0.888891,0.111109,0.000000	0.904865,0.095135,0.000000:0.888891,0.111109,0.000000	0.904865,0.095135,0.000000:0.888891,0.111109,0.000000	0.000007,0.543141,0.456852:0.000002,0.199997,0.800001	0.904865,0.095135,0.000000:0.888892,0.111108,0.000000	0.000000,0.229117,0.770883:0.000000,0.058822,0.941178	0.045152,0.954211,0.000637:0.038160,0.958794,0.003045	0.000599,0.999394,0.000006:0.000504,0.999465,0.000031	0.974389,0.025611,0.000000:0.969698,0.030302,0.000000	0.000005,0.543142,0.456853:0.000002,0.199997,0.800002	0.974389,0.025611,0.000000:0.969698,0.030302,0.000000	0.703916,0.296035,0.000050:0.666492,0.333243,0.000265	0.495544,0.416810,0.087646:0.333333,0.333333,0.333333
1	14001867	.	A	G	.	PASS	.	GL:GP	0.000407,0.698622,0.300971:0.000167,0.333276,0.666557	0.902773,0.097227,0.000000:0.888891,0.111109,0.000000	0.000645,0.698456,0.300899:0.000265,0.333243,0.666492	0.902773,0.097227,0.000000:0.888891,0.111109,0.000000	0.902773,0.097227,0.000000:0.888891,0.111109,0.000000	0.000006,0.998276,0.001719:0.000005,0.992066,0.007929	0.986717,0.013283,0.000000:0.984616,0.015384,0.000000	0.822776,0.177224,0.000000:0.800002,0.199997,0.000001	0.000003,0.537165,0.462832:0.000001,0.199997,0.800002	0.948903,0.051097,0.000000:0.941178,0.058822,0.000000	0.948903,0.051097,0.000000:0.941178,0.058822,0.000000	0.986717,0.013283,0.000000:0.984616,0.015384,0.000000	0.000000,0.537166,0.462833:0.000000,0.199997,0.800003	0.000060,0.999940,0.000000:0.000051,0.999949,0.000000	0.000079,0.999921,0.000000:0.000068,0.999932,0.000000	0.902773,0.097227,0.000000:0.888891,0.111109,0.000000	0.902773,0.097227,0.000000:0.888891,0.111109,0.000000	0.999159,0.000841,0.000000:0.999024,0.000976,0.000000	0.004641,0.995359,0.000000:0.004001,0.995999,0.000000	0.000645,0.698456,0.300899:0.000265,0.333243,0.666492	0.948903,0.051097,0.000000:0.941178,0.058822,0.000000	0.822774,0.177223,0.000002:0.799994,0.199995,0.000011	0.996646,0.003354,0.000000:0.996109,0.003891,0.000000	0.000000,0.008985,0.991015:0.000000,0.001949,0.998051	0.822776,0.177224,0.000000:0.800002,0.199997,0.000001	0.000000,0.367208,0.632792:0.000000,0.111109,0.888891	0.000000,0.999135,0.000865:0.000000,0.995998,0.004001	0.005821,0.994177,0.000002:0.005019,0.994970,0.000011	0.993314,0.006686,0.000000:0.992249,0.007751,0.000000	0.000000,0.999998,0.000002:0.000000,0.999992,0.000008	0.948903,0.051097,0.000000:0.941178,0.058822,0.000000	0.822776,0.177224,0.000001:0.800000,0.199997,0.000003	0.007316,0.992667,0.000017:0.006309,0.993611,0.000079
[capped]

Notice that the sampleDI simply an ind followed by and integer. These relate to the samples form the -b filelist

References