Change ploidy level in vcf file

Question

[young_bioinformatician]

Hello guys,

I have run freebayes for variant-calling and I forgot to set the ploidy parameter. Now my result is based on ploidy level 2, but I want to chage it to haploid. Is there any way to change diploid to haploid in VCF file instead re-running freebayes?

My final vcf file is recoded.

So It is like, 0/0, 0/1, 1/1 and so on...

Thanks.

[Pierre Lindenbaum]

with genotypes like 0/1, you'd better re-run freebayes...

[young_bioinformatician]

Thank you, Pierre. Uh how I made such a mistake.. Generating a new one takes 4 days...

I just checked and I have also raw vcf. Does it matter?

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  RUS_sieboldiana_3       QTP_myrtillacea_2       AMER_exigua     CHINA_baileyi   ASIA_integra    CHINA_tangii    CHINA_sinica_2  CHINA_shihtsuanensis_3  CHINA_wangiana  QTP_fargesii_2  QTP_spathulifolia       CHINA_taipaiensis       JAP_reinii_2    JAP_reinii      CHINA_permollis ASIA_gracilistyla       AMER_discolor  ASIA_pen CM018572.1      13      .       C       T       7.49335 .     AB=0;ABP=0;AC=2;AF=0.04;AN=50;AO=2;CIGAR=1X;DP=58;DPB=58;DPRA=0.857143;EPP=3.0103;EPPR=8.59409;GTI=1;LEN=1;MEANALT=1;MQM=39;MQMR=54.3214;NS=25;NUMALT=1;ODDS=1.42872;PAIRED=1;PAIREDR=0.75;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=2047;RO=56;RPL=0;RPP=7.35324;RPPR=124.613;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=22;SRP=8.59409;SRR=34;TYPE=snp;tech CM018572.1      19      .       C       T       6.04409 .       AB=0;ABP=0;AC=2;AF=0.0384615;AN=52;AO=2;CIGAR=1X;DP=60;DPB=60;DPRA=0.862069;EPP=7.35324;EPPR=8.40154;GTI=1;LEN=1;MEANALT=1;MQM=45;MQMR=54.2069;NS=26;NUMALT=1;ODDS=1.00425;PAIRED=1;PAIREDR=0.758621;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=2158;RO=58;RPL=0;RPP=7.35324;RPPR=112.183;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=23;SRP=8.40154;SRR=35;TY CM018572.1      20      .       T       A       6.95363 .       AB=0;ABP=0;AC=2;AF=0.0384615;AN=52;AO=2;CIGAR=1X;DP=60;DPB=60;DPRA=0.862069;EPP=3.0103;EPPR=8.40154;GTI=1;LEN=1;MEANALT=1;MQM=58;MQMR=53.7586;NS=26;NUMALT=1;ODDS=1.27433;PAIRED=1;PAIREDR=0.758621;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=2112;RO=58;RPL=0;RPP=7.35324;RPPR=104.246;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=22;SRP=10.3484;SRR=36;TYPE