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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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between pops with vcf? #34

Closed karenbobier closed 4 years ago

karenbobier commented 4 years ago

Hi Chase,

Is it possible to run the snpgenie_between_group.pl with vcf files rather than fasta files? I have two populations with variant data for 6 diploids per population and would like to estimate dn/ds between populations. If if cannot be run with vcfs do you have a tool you recommend for converting diploid vcf data to fasta format?

Thanks, Karen

singing-scientist commented 4 years ago

Greetings, Karen! Thanks for your interest in using SNPGenie.

I regret that I have not yet programmed a version of SNPGenie that uses the 'pooled' (SNP report/VCF-based) approach for estimating the between-group values—and will likely not get to this for some time.

However, I did recently write a Python script (generate_seqs_from_VCF.py) that randomly generates a user-specified number of sequences in a FASTA file, randomly distributing variants specified in a VCF at the appropriate frequencies. Two or more sets of sequences thus generated can then be used as input for the current SNPGenie between-group script.

The script, generate_seqs_from_VCF.py, requires the Python libraries SeqIO, os, random, re, and sys. It can be run like this:

generate_seqs_from_VCF.py [sequence file].fasta [SNP report].vcf [num sequences]

For the VCF file, the script simply uses the "AF" entry, and it should work as long as AF is present; for example, the following format:

##METADATA ROWS
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
NC_045512.2 643 .   C   A   148 PASS    DP=6102;AF=0.003114;SB=0;DP4=55,6026,0,20
NC_045512.2 689 .   T   C   170 PASS    DP=6604;AF=0.003028;SB=7;DP4=66,6509,1,19
NC_045512.2 716 .   A   G   173 PASS    DP=7833;AF=0.002936;SB=7;DP4=72,7736,1,22
NC_045512.2 769 .   T   C   203 PASS    DP=8319;AF=0.003005;SB=5;DP4=101,8192,1,24
NC_045512.2 778 .   T   C   167 PASS    DP=8091;AF=0.002719;SB=0;DP4=100,7964,0,22
...

For example, for a reference sequence in a file named reference.fasta, a VCF-format SNP report in a file named variants.vcf, and to create 1,000 sequences, one would run the following:

generate_seqs_from_VCF.py reference.fasta variants.vcf 1000

The script and full documentation have been added to Evolutionary Bioinformatics Toolkit. Please let me know if this addresses your request, and if you encounter any problems, as I have not tested this too extensively!

Best, Chase

karenbobier commented 4 years ago

Hi Chase,

Thanks for the quick reply. Your toolkit has been super useful.

I don't actually have pooled sequences, I have seperate variant data for each individual, currently all in one vcf but I can split it by population or individual. I do have the AF information in my vcfs but would you still recommend this for non-pooled data?

my vcf files look like this: 

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  ARG10   ARG18   ARG19   ARG21   ARG25   ARG27   ARG29   ARI10   ARI102  ARI11   ARI12   ARI4    ARI6
##contig=<ID=J9347376|m.109621,length=300>
J9347376|m.109621   72  .   G   T   307.47  .   AC=4;AF=0.222;AN=18;BaseQRankSum=0.871;ClippingRankSum=0.00;DP=66;ExcessHet=0.8432;FS=6.239;MLEAC=4;MLEAF=0.222;MQ=58.81;MQRankSum=0.967;QD=20.50;ReadPosRankSum=2.41;SOR=1.304 GT:AD:DP:GQ:PL  ./.:0,0:0:.:0,0,0   0/0:1,0:1:3:0,3,42  0/0:5,0:5:15:0,15,159   0/1:4,8:12:40:213,0,40  1/1:0,3:3:9:128,9,0 0/0:14,0:14:24:0,24,360 0/0:2,0:2:6:0,6,76  0/1:9,1:10:12:12,0,283  ./.:1,0:1:.:0,0,0   ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0   0/0:2,0:2:6:0,6,49  0/0:1,0:1:3:0,3,25
J9347376|m.109621   84  .   G   A   43.39   .   AC=1;AF=0.056;AN=18;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.056;MQ=60.00;MQRankSum=0.00;QD=14.46;ReadPosRankSum=0.967;SOR=0.223    GT:AD:DP:GQ:PL  ./.:0,0:0:.:0,0,0   0/0:1,0:1:3:0,3,42  0/0:3,0:3:9:0,9,115 0/0:8,0:8:24:0,24,342   0/1:1,2:3:36:75,0,36    0/0:9,0:9:27:0,27,362   0/0:2,0:2:6:0,6,76  0/0:9,0:9:15:0,15,225   0/0:1,0:1:3:0,3,38  ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0   0/0:1,0:1:3:0,3,25  ./.:0,0:0:.:0,0,0
J9347376|m.109621   129 .   C   A   230.12  .   AC=2;AF=0.125;AN=16;DP=31;ExcessHet=0.1703;FS=0.000;MLEAC=2;MLEAF=0.125;MQ=60.00;QD=27.00;SOR=1.329 GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,87  0/0:2,0:2:3:.:.:0,3,45  1/1:0,6:6:18:1|1:129_C_A:270,18,0   0/0:4,0:4:0:.:.:0,0,90  0/0:7,0:7:15:.:.:0,15,225   0/0:2,0:2:6:.:.:0,6,76  0/0:6,0:6:15:.:.:0,15,225   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,72  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0
J9347376|m.109621   135 .   C   G   1377.62 .   AC=16;AF=1.00;AN=16;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=16;MLEAF=1.00;MQ=60.00;QD=30.82;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL  ./.:0,0:0:.:.:.:0,0,0   1/1:0,2:2:6:.:.:87,6,0  1/1:0,2:2:6:.:.:80,6,0  1/1:0,6:6:18:1|1:129_C_A:270,18,0   1/1:0,6:6:21:.:.:295,21,0   1/1:0,7:7:21:.:.:287,21,0   1/1:0,1:1:3:.:.:42,3,0  1/1:0,6:6:18:.:.:253,18,0   ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0   1/1:0,2:2:6:.:.:87,6,0  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0
J9347376|m.109621   144 .   G   C   121.76  .   AC=1;AF=0.071;AN=14;BaseQRankSum=-9.210e-01;ClippingRankSum=0.00;DP=30;ExcessHet=3.3579;FS=0.000;MLEAC=1;MLEAF=0.071;MQ=53.67;MQRankSum=0.00;QD=15.22;ReadPosRankSum=0.732;SOR=0.799    GT:AD:DP:GQ:PL  ./.:0,0:0:.:0,0,0   0/0:2,0:2:6:0,6,74  0/0:1,0:1:3:0,3,42  0/0:3,0:3:0:0,0,39  0/1:3,5:8:99:150,0,101  0/0:5,0:5:15:0,15,202   ./.:2,0:2:.:0,0,0   0/0:7,0:7:0:0,0,211 ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0   0/0:2,0:2:6:0,6,76  ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0
J9347376|m.109621   210 .   G   A   3468.25 .   AC=9;AF=0.500;AN=18;BaseQRankSum=1.22;ClippingRankSum=0.00;DP=199;ExcessHet=7.7512;FS=5.817;MLEAC=11;MLEAF=0.611;MQ=52.40;MQRankSum=-1.360e+00;QD=18.16;ReadPosRankSum=0.203;SOR=0.415  GT:AD:DP:GQ:PL  ./.:0,0:0:.:0,0,0   0/0:3,0:3:0:0,0,28  1/1:1,8:9:17:224,17,0   1/1:3,54:57:99:1469,111,0   0/1:2,11:13:9:330,0,9   0/1:2,7:9:22:221,0,22   ./.:1,0:1:.:0,0,0   0/1:30,33:63:99:850,0,787   ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0   0/0:3,0:3:0:0,0,41  0/1:4,4:8:46:46,0,46    0/1:12,20:32:99:373,0,149
J9347376|m.109621   265 .   A   G   41.82   .   AC=1;AF=0.050;AN=20;BaseQRankSum=0.126;ClippingRankSum=0.00;DP=23;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.1793;MLEAC=1;MLEAF=0.050;MQ=60.00;MQRankSum=0.00;QD=8.36;ReadPosRankSum=-5.240e-01;SOR=0.223 GT:AD:DP:GQ:PL  0/0:1,0:1:3:0,3,27  0/0:1,0:1:3:0,3,38  0/0:3,0:3:9:0,9,117 0/0:2,0:2:6:0,6,80  0/1:2,3:5:37:73,0,37    0/0:3,0:3:6:0,6,90  0/0:1,0:1:3:0,3,32  0/0:3,0:3:9:0,9,117 0/0:3,0:3:9:0,9,58  ./.:0,0:0:.:0,0,0   0/0:1,0:1:3:0,3,27  ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0
J9347376|m.109621   279 .   G   C   49.24   .   AC=1;AF=0.050;AN=20;BaseQRankSum=0.967;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.1578;MLEAC=1;MLEAF=0.050;MQ=60.00;MQRankSum=0.00;QD=16.41;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL  0/0:1,0:1:3:.:.:0,3,27  0/0:1,0:1:3:.:.:0,3,38  0/0:3,0:3:9:.:.:0,9,117 0/0:2,0:2:6:.:.:0,6,80  0/0:4,0:4:12:.:.:0,12,158   0/1:1,2:3:75:0|1:279_G_C:81,0,75    0/0:1,0:1:3:.:.:0,3,32  0/0:3,0:3:9:.:.:0,9,117 0/0:4,0:4:12:.:.:0,12,93    ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,61  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0
J9347376|m.109621   282 .   C   A   49.24   .   AC=1;AF=0.050;AN=20;BaseQRankSum=0.431;ClippingRankSum=0.00;DP=24;ExcessHet=3.0103;FS=0.000;InbreedingCoeff=-0.1578;MLEAC=1;MLEAF=0.050;MQ=60.00;MQRankSum=0.00;QD=16.41;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PGT:PID:PL  0/0:1,0:1:3:.:.:0,3,27  0/0:1,0:1:3:.:.:0,3,38  0/0:3,0:3:9:.:.:0,9,117 0/0:2,0:2:6:.:.:0,6,80  0/0:4,0:4:12:.:.:0,12,158   0/1:1,2:3:75:0|1:279_G_C:81,0,75    0/0:1,0:1:3:.:.:0,3,32  0/0:3,0:3:9:.:.:0,9,117 0/0:4,0:4:12:.:.:0,12,93    ./.:0,0:0:.:.:.:0,0,0   0/0:2,0:2:6:.:.:0,6,61  ./.:0,0:0:.:.:.:0,0,0   ./.:0,0:0:.:.:.:0,0,0

Thanks, Karen

singing-scientist commented 4 years ago

Thanks for these additional details! I am not certain, but I believe you're simply saying that your VCF file is summarizing multiple individual sequences, and that the AF value here in the INFO columns represents a true allele frequency (I think, the allele frequency among all the samples in the columns that come after INFO). If that is true, and the AF represents the allele frequency in a group/sample/population of your organism of interest, then that is all I mean by a "pooled" approach, i.e., the VCF represents multiple individuals. In other words, it doesn't matter whether the sequence data were generated in a pooled fashion or summarized "after the fact" for multiple individual sequences. In summary, if the AF value represents the frequency you want represented in the FASTA, it should work!

It's entirely possible I misunderstood — please let me know!

Chase