Vcf

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 sampleID is simply an ind followed by an integer. These correspond to the samples from the -b filelist.

References