setting genotypes to missing

Question

[raalsuwaidi]

is there a tool to set a selection of genotypes to missing? that is replace the values by

like for example, this section of the VCF file, can i select a set of different POS and IDs and change the genotype values to . ?

chr5    97306635    rs112129873 A   AT  352.31  PASS    AC=0;AF=0.004167;AN=32;BaseQRankSum=-0.184;ClippingRankSum=0;DP=3230;ExcessHet=3.0103;FS=0;InbreedingCoeff=-0.0043;MLEAC=1;MLEAF=0.004167;MQ=60;MQRankSum=0;QD=19.57;ReadPosRankSum=1.13;SOR=0.387;VQSLOD=16.37;culprit=MQ;ASP;CAF=0.9994,0.000599;COMMON=1;GNO;KGPhase3;RS=112129873;RSPOS=97306635;SAO=0;SLO;SSR=0;TOPMED=0.99976904943934760,0.00023095056065239;VC=DIV;VP=0x050100000005000126000200;WGT=1;dbSNPBuildID=132;INS;VARTYPE=INS;EFF=INTERGENIC(MODIFIER||||||||)    GT:AD:DP:GQ:PL  0/0:36,0:36:94:0,94,1127    0/0:31,0:31:84:0,84,1260    0/0:25,0:25:60:0,60,900 0/0:27,0:27:63:0,63,945 0/0:38,0:38:99:0,99,1204    ./.:0,0:0:.:0,0,0   ./.:0,0:0:.:0,0,0   0/0:31,0:31:90:0,90,1350    0/0:27,0:27:70:0,70,897 ./.:0,0:0:.:0,0,0   0/0:20,0:20:60:0,60,644 0/0:23,0:23:60:0,60,900 ./.:0,0:0:.:0,0,0   0/0:19,0:19:51:0,51,765 0/0:24,0:24:72:0,72,776 0/0:31,0:31:90:0,90,1350    0/0:23,0:23:60:0,60,751 0/0:34,0:34:90:0,90,1350    0/0:18,0:18:51:0,51,7650/0:21,0:21:57:0,57,855

[Pierre Lindenbaum]

same as missing REF and ALT in vcf . Please edit your first question instead of asking a new one.

[raalsuwaidi]

when you look at the first question, it is clear that i still didnt get an answer. i thought maybe the question was in the wrong way, so i am writing it in another way. can you please help in answering it?

Answer 1

[atorreso]

You can use one of bcftools plugins.

For the example you gave:

bcftools +setGT input.vcf.gz -- -t q -i 'ID="rs112129873"' -n "./."

or

bcftools +setGT input.vcf.gz -- -t q -i 'POS=97306635' -n "./."

should do the job.

[raalsuwaidi]

thank you sooooo much