Using bcftools to change ploidy level in vcf files
1
0
Entering edit mode
4.0 years ago
flolil27 • 0

hello

I am facing problem with bcftools. I have a VCF file containing variants from a haploid fungus. I would like to use the --haploid2diploid option to convert haploid genotypes to homozygous diploid genotypes.

I have tried using bcftools convert --haploid2diploid -h hapfile.vcf > dipfile.vcf

but the dipfile.vcf is still a haploid vcf.

Does anyone know how I could do that with bcftools? Is there another way to convert my haploid vcf file?

Thanks

snp bcftools • 3.7k views
ADD COMMENT
0
Entering edit mode

Hi Flolil,

I am facing the same problem, did you find a solution?

Thanks, Elisabet

ADD REPLY
0
Entering edit mode
3.4 years ago

using vcffilterjdk: http://lindenb.github.io/jvarkit/VcfFilterJdk.html . It fix the haploid, genotype , AC and AN. I'm too lazty to fix things like AF (shouldn't change ?) , etc...

    $  wget -q -O - "https://raw.githubusercontent.com/CostaLab/practical_SS2015/598ea0dddf2ef073a55ae21bc6d39ac2172eb617/data_analysis/organisms/escherichia_coli/O157H7_Sakai/IonTorrentPGM_mem/SRX185723/SRR566635/SRR566635-snps.vcf" |\
       java -jar dist/vcffilterjdk.jar -e 'return new VariantContextBuilder(variant).genotypes(variant.getGenotypes().stream().map(G->!G.isCalled()?GenotypeBuilder.createMissing(G.getSampleName(),2):G).map(G->G.isCalled() && G.getPloidy()==1?new GenotypeBuilder(G).alleles(Arrays.asList(G.getAllele(0),G.getAllele(0))).make():G).collect(Collectors.toList())).attribute("AC",variant.getGenotypes().stream().mapToInt(G->G.isCalled() && G.getPloidy()==1 && !G.getAllele(0).isReference()?2:G.getAlleles().size()).sum()).attribute("AN",variant.getGenotypes().stream().mapToInt(G->G.isCalled() && G.getPloidy()==1 ?2:G.getAlleles().size()).sum()).make();'
    (...)

gi|15829254|ref|NC_002695.1|    270484  .   G   C   2747    .   AC=2;AF=1.00;AN=2;BaseQRankSum=1.612;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=3.4380;MLEAC=1;MLEAF=1.00;MQ=59.89;MQ0=0;MQRankSum=1.521;QD=23.68;ReadPosRankSum=-1.009;SOR=0.268 GT:AD:DP:GQ:PL  1/1:1,115:116:99:2777,0
gi|15829254|ref|NC_002695.1|    270502  .   G   A   2924    .   AC=2;AF=1.00;AN=2;BaseQRankSum=0.948;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=2.6493;MLEAC=1;MLEAF=1.00;MQ=59.26;MQ0=0;MQRankSum=1.667;QD=27.58;ReadPosRankSum=1.667;SOR=0.281  GT:AD:DP:GQ:PL  1/1:1,105:106:99:2954,0
gi|15829254|ref|NC_002695.1|    270545  .   A   C   2121    .   AC=2;AF=1.00;AN=2;BaseQRankSum=2.084;DP=109;Dels=0.01;FS=5.100;HaplotypeScore=23.5544;MLEAC=1;MLEAF=1.00;MQ=49.74;MQ0=3;MQRankSum=-1.031;QD=19.46;ReadPosRankSum=-0.760;SOR=0.425   GT:AD:DP:GQ:PL  1/1:5,103:108:99:2151,0
gi|15829254|ref|NC_002695.1|    270562  .   G   C   2366    .   AC=2;AF=1.00;AN=2;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=5.2793;MLEAC=1;MLEAF=1.00;MQ=48.85;MQ0=3;QD=22.75;SOR=0.818  GT:AD:DP:GQ:PL  1/1:1,103:104:99:2396,0
gi|15829254|ref|NC_002695.1|    270577  .   G   A   559 .   AC=2;AF=1.00;AN=2;BaseQRankSum=4.123;DP=63;Dels=0.00;FS=67.351;HaplotypeScore=61.7544;MLEAC=1;MLEAF=1.00;MQ=41.28;MQ0=3;MQRankSum=4.843;QD=8.87;ReadPosRankSum=-2.054;SOR=7.167 GT:AD:DP:GQ:PL  1/1:28,35:63:99:589,0
gi|15829254|ref|NC_002695.1|    270584  .   G   A   1197    .   AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=32.4027;MLEAC=1;MLEAF=1.00;MQ=38.79;MQ0=3;QD=21.00;SOR=0.931  GT:AD:DP:GQ:PL  1/1:0,57:57:99:1227,0
gi|15829254|ref|NC_002695.1|    270596  .   T   G   327 .   AC=2;AF=1.00;AN=2;BaseQRankSum=0.330;DP=51;Dels=0.02;FS=0.000;HaplotypeScore=28.8469;MLEAC=1;MLEAF=1.00;MQ=35.57;MQ0=3;MQRankSum=-0.578;QD=6.41;ReadPosRankSum=1.238;SOR=0.613  GT:AD:DP:GQ:PL  1/1:1,48:50:99:357,0
gi|15829254|ref|NC_002695.1|    270598  .   C   G   809 .   AC=2;AF=1.00;AN=2;BaseQRankSum=2.513;DP=52;Dels=0.02;FS=0.000;HaplotypeScore=29.6561;MLEAC=1;MLEAF=1.00;MQ=36.19;MQ0=3;MQRankSum=-0.852;QD=15.56;ReadPosRankSum=0.256;SOR=0.303 GT:AD:DP:GQ:PL  1/1:3,48:51:99:839,0
gi|15829254|ref|NC_002695.1|    270627  .   A   G   2705    .   AC=2;AF=1.00;AN=2;DP=103;Dels=0.01;FS=0.000;HaplotypeScore=5.0818;MLEAC=1;MLEAF=1.00;MQ=50.91;MQ0=2;QD=26.26;SOR=0.957  GT:AD:DP:GQ:PL  1/1:0,102:102:99:2735,0
gi|15829254|ref|NC_002695.1|    270646  .   C   A   2337    .   AC=2;AF=1.00;AN=2;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=7.7758;MLEAC=1;MLEAF=1.00;MQ=56.60;MQ0=0;QD=28.85;SOR=1.416   GT:AD:DP:GQ:PL  1/1:0,81:81:99:2367,0
ADD COMMENT

Login before adding your answer.

Traffic: 2498 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6