Question: Using bcftools to change ploidy level in vcf files
0
gravatar for flolil27
14 months ago by
flolil270
flolil270 wrote:

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 • 936 views
ADD COMMENTlink modified 7 months ago by Pierre Lindenbaum108k • written 14 months ago by flolil270

Hi Flolil,

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

Thanks, Elisabet

ADD REPLYlink written 7 months ago by elisabet.sjokvist0
0
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum108k wrote:

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 COMMENTlink modified 7 months ago • written 7 months ago by Pierre Lindenbaum108k
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